BMRBj - BMREntryMaster

Found 1 Document (0.622 seconds)

BMRB: 17840

2LHD

GB98 solution structure

Authors

He, Y., Chen, Y., Alexander, P., Bryan, P., Orban, J.

Assembly

GB98

Entity

1. GB98 (polymer, Thiol state: not present), 56 monomers, 6396.287 Da Detail

TTYKLILNLK QAKEEAIKEL VDAGTAEKYF KLIANAKTVE GVWTYKDEIK TFTVTE

Formula weight

6396.287 Da

Exptl. method

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 81.5 %, Completeness (bb): 98.8 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	81.5 % (556 of 682)	81.8 % (287 of 351)	78.6 % (213 of 271)	93.3 % (56 of 60)
Backbone	98.8 % (332 of 336)	99.1 % (113 of 114)	98.8 % (164 of 166)	98.2 % (55 of 56)
Sidechain	69.5 % (278 of 400)	73.4 % (174 of 237)	64.8 % (103 of 159)	25.0 % (1 of 4)
Aromatic	66.1 % (37 of 56)	78.6 % (22 of 28)	51.9 % (14 of 27)	100.0 % (1 of 1)
Methyl	67.5 % (54 of 80)	77.5 % (31 of 40)	57.5 % (23 of 40)

1. GB98

TTYKLILNLK QAKEEAIKEL VDAGTAEKYF KLIANAKTVE GVWTYKDEIK TFTVTE

Show sample condition

Sample

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 278 K, pH 7.0

#	Name	Isotope labeling	Type	Concentration
1	GB98	[U-100% 13C; U-100% 15N]		0.1 ~ 0.3 mM
2	potassium phosphate	natural abundance		100 mM
3	H2O	natural abundance		95 %
4	D2O	natural abundance		5 %

LACS Plot; CA

Referencing offset: -0.03 ppm, Outliers: 1 Detail

LACS Plot; CB

Referencing offset: -0.03 ppm, Outliers: 1 Detail

LACS Plot; HA

Referencing offset: -0.1 ppm, Outliers: 1 Detail

LACS Plot; CO

Referencing offset: 0.69 ppm, Outliers: 2 Detail

Protein Blocks Logo

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

Release date

2012-02-27

Citation

Mutational tipping points for switching protein folds and functions
He, Y., Chen, Y., Alexander, P., Bryan, P., Orban, J.
Structure (2012), 20, 283-291, PubMed 22325777 , DOI 10.1016/j.str.2011.11.018 , Abstract

Related entities 1. GB98, : 1 : 7 : 103 entities Detail

Experiments performed 10 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker DMX - 600 MHz with a Z axis gradient 1H/13C/15N triple resonance cryoprobe

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 278 K, pH 7.0

#	Name	Isotope labeling	Type	Concentration
1	GB98	[U-100% 13C; U-100% 15N]		0.1 ~ 0.3 mM
2	potassium phosphate	natural abundance		100 mM
3	H2O	natural abundance		95 %
4	D2O	natural abundance		5 %

2 3D CBCA(CO)NH

Instrument

Bruker DMX - 600 MHz with a Z axis gradient 1H/13C/15N triple resonance cryoprobe

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 278 K, pH 7.0

#	Name	Isotope labeling	Type	Concentration
1	GB98	[U-100% 13C; U-100% 15N]		0.1 ~ 0.3 mM
2	potassium phosphate	natural abundance		100 mM
3	H2O	natural abundance		95 %
4	D2O	natural abundance		5 %

3 3D HNCACB

Instrument

Bruker DMX - 600 MHz with a Z axis gradient 1H/13C/15N triple resonance cryoprobe

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 278 K, pH 7.0

#	Name	Isotope labeling	Type	Concentration
1	GB98	[U-100% 13C; U-100% 15N]		0.1 ~ 0.3 mM
2	potassium phosphate	natural abundance		100 mM
3	H2O	natural abundance		95 %
4	D2O	natural abundance		5 %

4 3D C(CO)NH

Instrument

Bruker DMX - 600 MHz with a Z axis gradient 1H/13C/15N triple resonance cryoprobe

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 278 K, pH 7.0

#	Name	Isotope labeling	Type	Concentration
1	GB98	[U-100% 13C; U-100% 15N]		0.1 ~ 0.3 mM
2	potassium phosphate	natural abundance		100 mM
3	H2O	natural abundance		95 %
4	D2O	natural abundance		5 %

5 3D HNCO

Instrument

Bruker DMX - 600 MHz with a Z axis gradient 1H/13C/15N triple resonance cryoprobe

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 278 K, pH 7.0

#	Name	Isotope labeling	Type	Concentration
1	GB98	[U-100% 13C; U-100% 15N]		0.1 ~ 0.3 mM
2	potassium phosphate	natural abundance		100 mM
3	H2O	natural abundance		95 %
4	D2O	natural abundance		5 %

6 3D 1H-15N NOESY

Instrument

Bruker DMX - 600 MHz with a Z axis gradient 1H/13C/15N triple resonance cryoprobe

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 278 K, pH 7.0

#	Name	Isotope labeling	Type	Concentration
1	GB98	[U-100% 13C; U-100% 15N]		0.1 ~ 0.3 mM
2	potassium phosphate	natural abundance		100 mM
3	H2O	natural abundance		95 %
4	D2O	natural abundance		5 %

7 3D 1H-13C NOESY aliphatic

Instrument

Bruker DMX - 600 MHz with a Z axis gradient 1H/13C/15N triple resonance cryoprobe

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 278 K, pH 7.0

#	Name	Isotope labeling	Type	Concentration
1	GB98	[U-100% 13C; U-100% 15N]		0.1 ~ 0.3 mM
2	potassium phosphate	natural abundance		100 mM
3	H2O	natural abundance		95 %
4	D2O	natural abundance		5 %

8 3D 1H-13C NOESY aromatic

Instrument

Bruker DMX - 600 MHz with a Z axis gradient 1H/13C/15N triple resonance cryoprobe

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 278 K, pH 7.0

#	Name	Isotope labeling	Type	Concentration
1	GB98	[U-100% 13C; U-100% 15N]		0.1 ~ 0.3 mM
2	potassium phosphate	natural abundance		100 mM
3	H2O	natural abundance		95 %
4	D2O	natural abundance		5 %

9 3D H(CCO)NH

Instrument

Bruker DMX - 600 MHz with a Z axis gradient 1H/13C/15N triple resonance cryoprobe

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 278 K, pH 7.0

#	Name	Isotope labeling	Type	Concentration
1	GB98	[U-100% 13C; U-100% 15N]		0.1 ~ 0.3 mM
2	potassium phosphate	natural abundance		100 mM
3	H2O	natural abundance		95 %
4	D2O	natural abundance		5 %

10 3D HBHA(CO)NH

Instrument

Bruker DMX - 600 MHz with a Z axis gradient 1H/13C/15N triple resonance cryoprobe

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 278 K, pH 7.0

#	Name	Isotope labeling	Type	Concentration
1	GB98	[U-100% 13C; U-100% 15N]		0.1 ~ 0.3 mM
2	potassium phosphate	natural abundance		100 mM
3	H2O	natural abundance		95 %
4	D2O	natural abundance		5 %

NMR combined restraints 5 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_17840_2lhd.nef
Input source #2: Coordindates	2lhd.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------
TTYKLILNLKQAKEEAIKELVDAGTAEKYFKLIANAKTVEGVWTYKDEIKTFTVTE
||||||||||||||||||||||||||||||||||||||||||||||||||||||||
TTYKLILNLKQAKEEAIKELVDAGTAEKYFKLIANAKTVEGVWTYKDEIKTFTVTE

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	56	0	0	100.0

Content subtype: combined_17840_2lhd.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	555		100.0 (chain: A, length: 56)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	Warning	811 (1)	noe	100.0 (chain: A, length: 56)
2	Distance restraints	CNS/XPLOR_distance_constraints_4	OK	63 (1)	hbond	66.1 (chain: A, length: 56)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_3	OK	66 (66)	.	87.5 (chain: A, length: 56)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 56, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 286
  - ¹³C chemical shifts: 213
  - ¹⁵N chemical shifts: 56
- Completeness of assignments
  - Entity_assemble_ID: A
- 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: 56, Sequence coverage: 100.0%
- Total number of restraints: 796
- Weight of restraints: 1.0 (796)
- Potential type of restraints: square-well-parabolic (796)
- Range of distance target values: 2.4, 4.4 (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_4
  - Status: OK
  - Experiment type: hbond
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 56, Sequence coverage: 66.1%
  - Total number of restraints: 63
  - Weight of restraints: 1.0 (63)
  - Potential type of restraints: square-well-parabolic (63)
  - Range of distance target values: 2.0, 2.9 (Å)
  - Histogram of 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: 56, Sequence coverage: 87.5%
- Total number of restraints: 66
- Total number of restraints per polymer type: 66
- Weight of restraints: 1.0 (66)
- Potential type of restraints: square-well-parabolic (66)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords De Novo protein