BMRBj - BMREntryMaster

Found 1 Document (0.912 seconds)

BMRB: 15956

2K3G

NMR structure analysis of a BMP receptor

Authors

Klages, J., Kotzsch, A., Mueller, T., Kessler, H.

Assembly

BMPR-IA

Entity

1. BMPR-IA (polymer, Thiol state: all disulfide bound), 102 monomers, 11268.61 Da Detail

GPEDTLPFLK CYCSGHCPDD AINNTCITNG HCFAIIEEDD QGETTLASGC MKYEGSDFQC KDSPKAQLRR TIECCRTNLC NQYLQPTLPP VVIGPFFDGS IR

Formula weight

11268.61 Da

Source organism

Exptl. method

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 98.0 %, Completeness: 89.5 %, Completeness (bb): 94.1 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	89.5 % (1020 of 1140)	91.2 % (542 of 594)	86.0 % (380 of 442)	94.2 % (98 of 104)
Backbone	94.1 % (561 of 596)	95.6 % (195 of 204)	93.3 % (278 of 298)	93.6 % (88 of 94)
Sidechain	86.5 % (552 of 638)	89.0 % (347 of 390)	81.9 % (195 of 238)	100.0 % (10 of 10)
Aromatic	22.0 % (18 of 82)	43.9 % (18 of 41)	0.0 % (0 of 41)
Methyl	96.6 % (85 of 88)	95.5 % (42 of 44)	97.7 % (43 of 44)

1. Bone Morphogenetic Protein Receptor Type IA

GPEDTLPFLK CYCSGHCPDD AINNTCITNG HCFAIIEEDD QGETTLASGC MKYEGSDFQC KDSPKAQLRR TIECCRTNLC NQYLQPTLPP VVIGPFFDGS IR

Show sample condition

Sample #1

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.3, Details pH 6.3

#	Name	Isotope labeling	Type	Concentration
1	Bone Morphogenetic Protein Receptor Type IA	[U-99% 15N]		1.1 mM
2	H2O	natural abundance		95 %
3	D2O	natural abundance		5 %
4	potassium phosphate	natural abundance		10 mM
5	sodium azide	natural abundance		0.2 w/v

Sample #2

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.3, Details pH 6.3

#	Name	Isotope labeling	Type	Concentration
6	Bone Morphogenetic Protein Receptor Type IA	[U-94% 13C; U-98% 15N]		0.5 mM
7	H2O	natural abundance		95 %
8	D2O	natural abundance		5 %
9	potassium phosphate	natural abundance		10 mM
10	sodium azide	natural abundance		0.2 w/v

LACS Plot; CA

Referencing offset: -0.38 ppm, Outliers: 1 Detail

LACS Plot; CB

Referencing offset: -0.38 ppm, Outliers: 1 Detail

LACS Plot; HA

Referencing offset: 0.1 ppm, Outliers: 3 Detail

LACS Plot; CO

Referencing offset: 3.31 ppm, Outliers: 1 Detail

Protein Blocks Logo

Calculated from 21 models in PDB: 2K3G, Strand ID: A Detail

Release date

2009-02-09

Citation

The solution structure of BMPR-IA reveals a local disorder-to-order transition upon BMP-2 binding
Klages, J., Kotzsch, A., Coles, M., Nickel, J., Mueller, T., Kessler, H.
Biochemistry (2008), 47, 11930-11939, PubMed 18937504 , DOI 10.1021/bi801059j , Abstract

Related entities 1. BMPR-IA, : 1 : 11 : 27 entities Detail

Interaction partners 1. BMPR-IA, : 32 interactors Detail

More details for 32 interactors identified by 9 citations

Experiments performed 20 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker DMX - 750 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.3, Details pH 6.3

#	Name	Isotope labeling	Type	Concentration
6	Bone Morphogenetic Protein Receptor Type IA	[U-94% 13C; U-98% 15N]		0.5 mM
7	H2O	natural abundance		95 %
8	D2O	natural abundance		5 %
9	potassium phosphate	natural abundance		10 mM
10	sodium azide	natural abundance		0.2 w/v

2 2D 1H-13C HSQC

Instrument

Bruker DMX - 750 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.3, Details pH 6.3

#	Name	Isotope labeling	Type	Concentration
6	Bone Morphogenetic Protein Receptor Type IA	[U-94% 13C; U-98% 15N]		0.5 mM
7	H2O	natural abundance		95 %
8	D2O	natural abundance		5 %
9	potassium phosphate	natural abundance		10 mM
10	sodium azide	natural abundance		0.2 w/v

3 3D HNCO

Instrument

Bruker DMX - 750 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.3, Details pH 6.3

#	Name	Isotope labeling	Type	Concentration
6	Bone Morphogenetic Protein Receptor Type IA	[U-94% 13C; U-98% 15N]		0.5 mM
7	H2O	natural abundance		95 %
8	D2O	natural abundance		5 %
9	potassium phosphate	natural abundance		10 mM
10	sodium azide	natural abundance		0.2 w/v

4 3D HNCA

Instrument

Bruker DMX - 750 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.3, Details pH 6.3

#	Name	Isotope labeling	Type	Concentration
6	Bone Morphogenetic Protein Receptor Type IA	[U-94% 13C; U-98% 15N]		0.5 mM
7	H2O	natural abundance		95 %
8	D2O	natural abundance		5 %
9	potassium phosphate	natural abundance		10 mM
10	sodium azide	natural abundance		0.2 w/v

5 3D CBCA(CO)NH

Instrument

Bruker DMX - 750 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.3, Details pH 6.3

#	Name	Isotope labeling	Type	Concentration
6	Bone Morphogenetic Protein Receptor Type IA	[U-94% 13C; U-98% 15N]		0.5 mM
7	H2O	natural abundance		95 %
8	D2O	natural abundance		5 %
9	potassium phosphate	natural abundance		10 mM
10	sodium azide	natural abundance		0.2 w/v

6 3D HBHA(CO)NH

Instrument

Bruker DMX - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.3, Details pH 6.3

#	Name	Isotope labeling	Type	Concentration
6	Bone Morphogenetic Protein Receptor Type IA	[U-94% 13C; U-98% 15N]		0.5 mM
7	H2O	natural abundance		95 %
8	D2O	natural abundance		5 %
9	potassium phosphate	natural abundance		10 mM
10	sodium azide	natural abundance		0.2 w/v

7 3D HNCACB

Instrument

Bruker DMX - 750 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.3, Details pH 6.3

#	Name	Isotope labeling	Type	Concentration
6	Bone Morphogenetic Protein Receptor Type IA	[U-94% 13C; U-98% 15N]		0.5 mM
7	H2O	natural abundance		95 %
8	D2O	natural abundance		5 %
9	potassium phosphate	natural abundance		10 mM
10	sodium azide	natural abundance		0.2 w/v

8 3D C(CO)NH

Instrument

Bruker DMX - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.3, Details pH 6.3

#	Name	Isotope labeling	Type	Concentration
6	Bone Morphogenetic Protein Receptor Type IA	[U-94% 13C; U-98% 15N]		0.5 mM
7	H2O	natural abundance		95 %
8	D2O	natural abundance		5 %
9	potassium phosphate	natural abundance		10 mM
10	sodium azide	natural abundance		0.2 w/v

9 3D HCCH-TOCSY

Instrument

Bruker DMX - 750 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.3, Details pH 6.3

#	Name	Isotope labeling	Type	Concentration
6	Bone Morphogenetic Protein Receptor Type IA	[U-94% 13C; U-98% 15N]		0.5 mM
7	H2O	natural abundance		95 %
8	D2O	natural abundance		5 %
9	potassium phosphate	natural abundance		10 mM
10	sodium azide	natural abundance		0.2 w/v

10 3D HNHA

Instrument

Bruker DMX - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.3, Details pH 6.3

#	Name	Isotope labeling	Type	Concentration
1	Bone Morphogenetic Protein Receptor Type IA	[U-99% 15N]		1.1 mM
2	H2O	natural abundance		95 %
3	D2O	natural abundance		5 %
4	potassium phosphate	natural abundance		10 mM
5	sodium azide	natural abundance		0.2 w/v

11 2D 1H-1H NOESY

Instrument

Bruker Avance - 900 MHz equipped with cryo probe

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.3, Details pH 6.3

#	Name	Isotope labeling	Type	Concentration
6	Bone Morphogenetic Protein Receptor Type IA	[U-94% 13C; U-98% 15N]		0.5 mM
7	H2O	natural abundance		95 %
8	D2O	natural abundance		5 %
9	potassium phosphate	natural abundance		10 mM
10	sodium azide	natural abundance		0.2 w/v

12 3D 1H-15N NOESY

Instrument

Bruker Avance - 900 MHz equipped with cryo probe

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.3, Details pH 6.3

#	Name	Isotope labeling	Type	Concentration
6	Bone Morphogenetic Protein Receptor Type IA	[U-94% 13C; U-98% 15N]		0.5 mM
7	H2O	natural abundance		95 %
8	D2O	natural abundance		5 %
9	potassium phosphate	natural abundance		10 mM
10	sodium azide	natural abundance		0.2 w/v

13 3D 1H-13C NOESY

Instrument

Bruker Avance - 900 MHz equipped with cryo probe

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.3, Details pH 6.3

#	Name	Isotope labeling	Type	Concentration
6	Bone Morphogenetic Protein Receptor Type IA	[U-94% 13C; U-98% 15N]		0.5 mM
7	H2O	natural abundance		95 %
8	D2O	natural abundance		5 %
9	potassium phosphate	natural abundance		10 mM
10	sodium azide	natural abundance		0.2 w/v

14 3D HNHB

Instrument

Bruker DMX - 750 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.3, Details pH 6.3

#	Name	Isotope labeling	Type	Concentration
1	Bone Morphogenetic Protein Receptor Type IA	[U-99% 15N]		1.1 mM
2	H2O	natural abundance		95 %
3	D2O	natural abundance		5 %
4	potassium phosphate	natural abundance		10 mM
5	sodium azide	natural abundance		0.2 w/v

15 3D HCCH-COSY

Instrument

Bruker DMX - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.3, Details pH 6.3

#	Name	Isotope labeling	Type	Concentration
6	Bone Morphogenetic Protein Receptor Type IA	[U-94% 13C; U-98% 15N]		0.5 mM
7	H2O	natural abundance		95 %
8	D2O	natural abundance		5 %
9	potassium phosphate	natural abundance		10 mM
10	sodium azide	natural abundance		0.2 w/v

16 3D 1H-15N-15N NOESY

Instrument

Bruker Avance - 900 MHz equipped with cryo probe

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.3, Details pH 6.3

#	Name	Isotope labeling	Type	Concentration
6	Bone Morphogenetic Protein Receptor Type IA	[U-94% 13C; U-98% 15N]		0.5 mM
7	H2O	natural abundance		95 %
8	D2O	natural abundance		5 %
9	potassium phosphate	natural abundance		10 mM
10	sodium azide	natural abundance		0.2 w/v

17 3D 1H-15N-13C NIOESY

Instrument

Bruker Avance - 900 MHz equipped with cryo probe

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.3, Details pH 6.3

#	Name	Isotope labeling	Type	Concentration
6	Bone Morphogenetic Protein Receptor Type IA	[U-94% 13C; U-98% 15N]		0.5 mM
7	H2O	natural abundance		95 %
8	D2O	natural abundance		5 %
9	potassium phosphate	natural abundance		10 mM
10	sodium azide	natural abundance		0.2 w/v

18 3D HCCH-TOCSY

Instrument

Bruker DMX - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.3, Details pH 6.3

#	Name	Isotope labeling	Type	Concentration
6	Bone Morphogenetic Protein Receptor Type IA	[U-94% 13C; U-98% 15N]		0.5 mM
7	H2O	natural abundance		95 %
8	D2O	natural abundance		5 %
9	potassium phosphate	natural abundance		10 mM
10	sodium azide	natural abundance		0.2 w/v

19 3D HN(CA)HA

Instrument

Bruker DMX - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.3, Details pH 6.3

#	Name	Isotope labeling	Type	Concentration
6	Bone Morphogenetic Protein Receptor Type IA	[U-94% 13C; U-98% 15N]		0.5 mM
7	H2O	natural abundance		95 %
8	D2O	natural abundance		5 %
9	potassium phosphate	natural abundance		10 mM
10	sodium azide	natural abundance		0.2 w/v

20 3D HN(CA)CO

Instrument

Bruker DMX - 750 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.3, Details pH 6.3

#	Name	Isotope labeling	Type	Concentration
6	Bone Morphogenetic Protein Receptor Type IA	[U-94% 13C; U-98% 15N]		0.5 mM
7	H2O	natural abundance		95 %
8	D2O	natural abundance		5 %
9	potassium phosphate	natural abundance		10 mM
10	sodium azide	natural abundance		0.2 w/v

NMR combined restraints 6 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_15956_2k3g.nef
Input source #2: Coordindates	2k3g.cif
Diamagnetism of the molecular assembly	True (excluding Oxygen atoms)
Whether the assembly has a disulfide bond	True (see coordinates for details)
Whether the assembly has a other bond	None
Whether the assembly contains a cyclic polymer	None
Overall data processing status	Warning

Disulfide bonds

Ptnr_site_1	Ptnr_site_2	Redox_state_prediction_1	Redox_state_prediction_2	Distance (Å)
A:38:CYS:SG	A:59:CYS:SG	oxidized, CA 51.95, CB 41.36 ppm	oxidized, CA 52.34, CB 36.95 ppm	1.988
A:40:CYS:SG	A:44:CYS:SG	oxidized, CA 53.85, CB 48.92 ppm	unknown	2.021
A:53:CYS:SG	A:77:CYS:SG	oxidized, CA 52.56, CB 48.65 ppm	oxidized, CA 60.03, CB 46.1 ppm	2.026
A:87:CYS:SG	A:101:CYS:SG	oxidized, CA 56.81, CB 40.78 ppm	oxidized, CA 55.01, CB 45.32 ppm	2.023
A:102:CYS:SG	A:107:CYS:SG	oxidized, CA 56.18, CB 46.09 ppm	oxidized, CA 58.37, CB 46.09 ppm	2.021

Other bonds (neither disulfide, covalent nor hydrogen bonds, e.g. Zinc–sulphur bond)

None

Non-standard residues

None

Sequence alignments

Entity_assembly_ID (NMR): A vs Auth_asym_ID (model): A

--30-------40--------50--------60--------70--------80--------90-------100-------110-------120-------
GPEDTLPFLKCYCSGHCPDDAINNTCITNGHCFAIIEEDDQGETTLASGCMKYEGSDFQCKDSPKAQLRRTIECCRTNLCNQYLQPTLPPVVIGPFFDGS
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
GPEDTLPFLKCYCSGHCPDDAINNTCITNGHCFAIIEEDDQGETTLASGCMKYEGSDFQCKDSPKAQLRRTIECCRTNLCNQYLQPTLPPVVIGPFFDGS
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100

--
IR
||
IR
--

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	102	0	0	100.0

Content subtype: combined_15956_2k3g.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Covalent bonds	assembly	OK	5		No information
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	1020		98.0 (chain: A, length: 102)
1	Distance restraints	CNS/XPLOR_distance_constraints_4	Warning	817 (1)	noe	99.0 (chain: A, length: 102)
2	Distance restraints	CNS/XPLOR_distance_constraints_5	Warning	5 (1)	undefined	9.8 (chain: A, length: 102)
3	Distance restraints	CNS/XPLOR_distance_constraints_6	Warning	44 (1)	hbond	28.4 (chain: A, length: 102)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_3	Warning	175 (175)	.	77.5 (chain: A, length: 102)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 102, Sequence coverage: 98.0%
- Total number of assignments
  - ¹H chemical shifts: 540
  - ¹³C chemical shifts: 379
  - ¹⁵N chemical shifts: 101
- Completeness of assignments
  - Entity_assemble_ID: A
- Redox state of CYS
- Peptide bond of PRO
- Rotameric state of ILE , LEU, and VAL
- Histogram of normalized assigned chemical shifts
- Random coil index and derived parameters (S² and NMR RMSD)
  - Chain_ID: A

Covalent bonds

Saveframe: assembly
- Status: OK

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_4
- Status: Warning
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 102, Sequence coverage: 99.0%
- Total number of restraints: 815
- Weight of restraints: 1.0 (815)
- Potential type of restraints: square-well-parabolic (815)
- Range of distance target values: 1.15, 7.5 (Å)
- Histogram of distance target values
- Histogram of discrepancy in distance target values
- Distance restraints per residue
  - Chain_ID: A
- Distance restraints on contact map
- Saveframe: CNS/XPLOR_distance_constraints_5
  - Status: Warning
  - Experiment type: undefined
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 102, Sequence coverage: 9.8%
  - Total number of restraints: 5
  - Weight of restraints: 1.0 (5)
  - Potential type of restraints: square-well-parabolic (5)
  - Range of distance target values: 2.02, 2.02 (Å)
  - Distance restraints per residue
    - Chain_ID: A
  - Distance restraints on contact map
  - Saveframe: CNS/XPLOR_distance_constraints_6
    - Status: Warning
    - Experiment type: hbond
    - Sequence coverage of experimental data
      - Entity_assembly_ID: A, Chain length: 102, Sequence coverage: 28.4%
    - Total number of restraints: 44
    - Weight of restraints: 1.0 (44)
    - Potential type of restraints: square-well-parabolic (44)
    - Range of distance target values: 2.1, 3.05 (Å)
    - Histogram of distance target values
    - Histogram of discrepancy in distance target values
    - Distance restraints per residue
      - Chain_ID: A
    - Distance restraints on contact map

Dihedral angle restraints

Saveframe: CNS/XPLOR_dihedral_3
- Status: Warning
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 102, Sequence coverage: 77.5%
- Total number of restraints: 175
- Total number of restraints per polymer type: 175
- Weight of restraints: 1.0 (175)
- Potential type of restraints: square-well-parabolic (175)
- Plot of Phi-Psi angle restraints
- Plot of Chi1-Chi2 angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords Bone Morphogenetic Protein Receptor type IA, induced fit, molecular recognition, NMR, BMP, NMR structure, receptor, TGF-beta superfamily