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BMRB: 16637

2KJD

Solution Structure of extended PDZ2 Domain from NHERF1 (150-270)

Authors

Bhattacharya, S., Dai, Z., Li, J., Baxter, S., Callaway, D.J.E., Cowburn, D., Bu, Z.

Assembly

PDZ2-270

Entity

1. PDZ2-270 (polymer, Thiol state: all free), 128 monomers, 14079.79 Da Detail

GIDPFTMLRP RLCTMKKGPS GYGFNLHSDK SKPGQFIRSV DPDSPAEASG LRAQDRIVEV NGVCMEGKQH GDVVSAIRAG GDETKLLVVD RETDEFFKKC RVIPSQEHLN GPLPVPFTNG EIQKENSR

Formula weight

14079.79 Da

Source organism

Exptl. method

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 91.8 %, Completeness (bb): 95.1 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	91.8 % (1343 of 1463)	93.1 % (719 of 772)	89.0 % (501 of 563)	96.1 % (123 of 128)
Backbone	95.1 % (711 of 748)	95.4 % (247 of 259)	94.6 % (351 of 371)	95.8 % (113 of 118)
Sidechain	90.0 % (747 of 830)	92.0 % (472 of 513)	86.3 % (265 of 307)	100.0 % (10 of 10)
Aromatic	68.8 % (55 of 80)	87.5 % (35 of 40)	50.0 % (20 of 40)
Methyl	97.4 % (113 of 116)	98.3 % (57 of 58)	96.6 % (56 of 58)

1. PDZ2-270

GIDPFTMLRP RLCTMKKGPS GYGFNLHSDK SKPGQFIRSV DPDSPAEASG LRAQDRIVEV NGVCMEGKQH GDVVSAIRAG GDETKLLVVD RETDEFFKKC RVIPSQEHLN GPLPVPFTNG EIQKENSR

Show sample condition

Sample

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303 K, pH 7.5

#	Name	Isotope labeling	Type	Concentration
1	PDZ2-270	[U-100% 13C; U-100% 15N]		550 uM
2	HEPES	natural abundance		20 mM
3	DTT	natural abundance		0.5 mM
4	PMSF	natural abundance		0.1 mM
5	sodium chloride	natural abundance		150 mM

LACS Plot; CA

Referencing offset: -0.13 ppm, Outliers: 2 Detail

LACS Plot; CB

Referencing offset: -0.13 ppm, Outliers: 2 Detail

LACS Plot; HA

Referencing offset: -0.05 ppm, Outliers: 2 Detail

LACS Plot; CO

Referencing offset: -0.11 ppm, Outliers: 4 Detail

Protein Blocks Logo

Calculated from 20 models in PDB: 2KJD, Strand ID: A Detail

Release date

2010-01-31

Citation

A conformational switch in the scaffolding protein NHERF1 controls autoinhibition and complex formation
Bhattacharya, S., Dai, Z., Li, J., Baxter, S., Callaway, D.J.E., Cowburn, D., Bu, Z.
J. Biol. Chem. (2010), 285, 9981-9994, PubMed 20042604 , DOI 10.1074/jbc.M109.074005 , Abstract

Related entities 1. PDZ2-270, : 1 : 2 : 3 : 72 entities Detail

Interaction partners 1. PDZ2-270, : 35 interactors Detail

More details for 35 interactors identified by 22 citations

Experiments performed 7 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303 K, pH 7.5

#	Name	Isotope labeling	Type	Concentration
1	PDZ2-270	[U-100% 13C; U-100% 15N]		550 uM
2	HEPES	natural abundance		20 mM
3	DTT	natural abundance		0.5 mM
4	PMSF	natural abundance		0.1 mM
5	sodium chloride	natural abundance		150 mM

2 2D 1H-13C HSQC

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303 K, pH 7.5

#	Name	Isotope labeling	Type	Concentration
1	PDZ2-270	[U-100% 13C; U-100% 15N]		550 uM
2	HEPES	natural abundance		20 mM
3	DTT	natural abundance		0.5 mM
4	PMSF	natural abundance		0.1 mM
5	sodium chloride	natural abundance		150 mM

3 3D HNCACB

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303 K, pH 7.5

#	Name	Isotope labeling	Type	Concentration
1	PDZ2-270	[U-100% 13C; U-100% 15N]		550 uM
2	HEPES	natural abundance		20 mM
3	DTT	natural abundance		0.5 mM
4	PMSF	natural abundance		0.1 mM
5	sodium chloride	natural abundance		150 mM

4 3D HCCH-TOCSY

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303 K, pH 7.5

#	Name	Isotope labeling	Type	Concentration
1	PDZ2-270	[U-100% 13C; U-100% 15N]		550 uM
2	HEPES	natural abundance		20 mM
3	DTT	natural abundance		0.5 mM
4	PMSF	natural abundance		0.1 mM
5	sodium chloride	natural abundance		150 mM

5 3D H(CCO)NH

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303 K, pH 7.5

#	Name	Isotope labeling	Type	Concentration
1	PDZ2-270	[U-100% 13C; U-100% 15N]		550 uM
2	HEPES	natural abundance		20 mM
3	DTT	natural abundance		0.5 mM
4	PMSF	natural abundance		0.1 mM
5	sodium chloride	natural abundance		150 mM

6 3D 1H-15N NOESY

Instrument

Bruker Avance - 900 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303 K, pH 7.5

#	Name	Isotope labeling	Type	Concentration
1	PDZ2-270	[U-100% 13C; U-100% 15N]		550 uM
2	HEPES	natural abundance		20 mM
3	DTT	natural abundance		0.5 mM
4	PMSF	natural abundance		0.1 mM
5	sodium chloride	natural abundance		150 mM

7 3D 1H-13C NOESY

Instrument

Bruker Avance - 900 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303 K, pH 7.5

#	Name	Isotope labeling	Type	Concentration
1	PDZ2-270	[U-100% 13C; U-100% 15N]		550 uM
2	HEPES	natural abundance		20 mM
3	DTT	natural abundance		0.5 mM
4	PMSF	natural abundance		0.1 mM
5	sodium chloride	natural abundance		150 mM

NMR combined restraints 4 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_16637_2kjd.nef
Input source #2: Coordindates	2kjd.cif
Diamagnetism of the molecular assembly	True (excluding Oxygen atoms)
Whether the assembly has a disulfide bond	None
Whether the assembly has a other bond	None
Whether the assembly contains a cyclic polymer	None
Overall data processing status	Warning

Disulfide bonds

None

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

--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100
GIDPFTMLRPRLCTMKKGPSGYGFNLHSDKSKPGQFIRSVDPDSPAEASGLRAQDRIVEVNGVCMEGKQHGDVVSAIRAGGDETKLLVVDRETDEFFKKC
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
GIDPFTMLRPRLCTMKKGPSGYGFNLHSDKSKPGQFIRSVDPDSPAEASGLRAQDRIVEVNGVCMEGKQHGDVVSAIRAGGDETKLLVVDRETDEFFKKC

-------110-------120--------
RVIPSQEHLNGPLPVPFTNGEIQKENSR
||||||||||||||||||||||||||||
RVIPSQEHLNGPLPVPFTNGEIQKENSR

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	128	0	0	100.0

Content subtype: combined_16637_2kjd.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	1345		99.2 (chain: A, length: 128)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	Warning	3076 (1)	noe	95.3 (chain: A, length: 128)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_3	OK	116 (116)	.	62.5 (chain: A, length: 128)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 128, Sequence coverage: 99.2%
- Total number of assignments
  - ¹H chemical shifts: 727
  - ¹³C chemical shifts: 495
  - ¹⁵N chemical shifts: 123
- Completeness of assignments
  - Entity_assemble_ID: A
- Redox state of CYS
- Peptide bond of PRO
- Tautomeric state of HIS
- 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

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_2
- Status: Warning
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 128, Sequence coverage: 95.3%
- Total number of restraints: 3076
- Weight of restraints: 1.0 (3076)
- Potential type of restraints: square-well-parabolic (3076)
- Range of distance target values: 2.19, 4.15 (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: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 128, Sequence coverage: 62.5%
- Total number of restraints: 116
- Total number of restraints per polymer type: 116
- Weight of restraints: 1.0 (116)
- Potential type of restraints: square-well-parabolic (116)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords NHERF1, PDZ, PDZ domain, PROTEIN