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BMRB: 16117

2KDM

NMR structures of GA95 and GB95, two designed proteins with 95% sequence identity but different folds and functions

Authors

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

Assembly

Gb95

Entity

1. Gb95 (polymer, Thiol state: not present), 56 monomers, 6354.207 Da Detail

TTYKLILNLK QAKEEAIKEA VDAGTAEKYF KLIANAKTVE GVWTYKDEIK TFTVTE

Formula weight

6354.207 Da

Exptl. method

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 89.5 %, Completeness (bb): 98.8 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	89.5 % (604 of 675)	86.5 % (300 of 347)	91.4 % (245 of 268)	98.3 % (59 of 60)
Backbone	98.8 % (332 of 336)	99.1 % (113 of 114)	98.8 % (164 of 166)	98.2 % (55 of 56)
Sidechain	83.0 % (326 of 393)	80.3 % (187 of 233)	86.5 % (135 of 156)	100.0 % (4 of 4)
Aromatic	82.1 % (46 of 56)	82.1 % (23 of 28)	81.5 % (22 of 27)	100.0 % (1 of 1)
Methyl	80.8 % (63 of 78)	82.1 % (32 of 39)	79.5 % (31 of 39)

1. entity

TTYKLILNLK QAKEEAIKEA VDAGTAEKYF KLIANAKTVE GVWTYKDEIK TFTVTE

Show sample condition

Sample

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293 (±0.1) K, pH 7.2 (±0.1), Details 0.15~0.3 mM Gb95 protein + pH7.2 100 mM potassium phosphate + 10% D2O

#	Name	Isotope labeling	Type	Concentration
1	Gb95	[U-100% 13C; U-100% 15N]		0.15-0.3 mM
2	potassium phosphate pH 7.2	natural abundance		100 mM
3	H2O	natural abundance		90 %
4	D2O	natural abundance		10 %

LACS Plot; CA

Referencing offset: 0.02 ppm, Outliers: 1 Detail

LACS Plot; CB

Referencing offset: 0.02 ppm, Outliers: 1 Detail

LACS Plot; HA

Referencing offset: -0.23 ppm, Outliers: 1 Detail

LACS Plot; CO

Referencing offset: 0.09 ppm, Outliers: 2 Detail

Protein Blocks Logo

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

Release date

2010-01-11

Citation

De novo structure generation using chemical shifts for proteins with high-sequence identity but different folds
Shen, Y., Bryan, P.N., He, Y., Orban, J., Baker, D., Bax, A.
Protein Sci. (2010), 19, 349-356, PubMed 19998407 , DOI 10.1002/pro.303 , Abstract

Related entities 1. Gb95, : 1 : 7 : 103 entities Detail

Experiments performed 10 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker DRX - 600 MHz with a z-axis gradient triple-resonance cryoprobe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293 (±0.1) K, pH 7.2 (±0.1), Details 0.15~0.3 mM Gb95 protein + pH7.2 100 mM potassium phosphate + 10% D2O

#	Name	Isotope labeling	Type	Concentration
1	Gb95	[U-100% 13C; U-100% 15N]		0.15-0.3 mM
2	potassium phosphate pH 7.2	natural abundance		100 mM
3	H2O	natural abundance		90 %
4	D2O	natural abundance		10 %

2 3D HNCACB

Instrument

Bruker DRX - 600 MHz with a z-axis gradient triple-resonance cryoprobe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293 (±0.1) K, pH 7.2 (±0.1), Details 0.15~0.3 mM Gb95 protein + pH7.2 100 mM potassium phosphate + 10% D2O

#	Name	Isotope labeling	Type	Concentration
1	Gb95	[U-100% 13C; U-100% 15N]		0.15-0.3 mM
2	potassium phosphate pH 7.2	natural abundance		100 mM
3	H2O	natural abundance		90 %
4	D2O	natural abundance		10 %

3 3D CBCA(CO)NH

Instrument

Bruker DRX - 600 MHz with a z-axis gradient triple-resonance cryoprobe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293 (±0.1) K, pH 7.2 (±0.1), Details 0.15~0.3 mM Gb95 protein + pH7.2 100 mM potassium phosphate + 10% D2O

#	Name	Isotope labeling	Type	Concentration
1	Gb95	[U-100% 13C; U-100% 15N]		0.15-0.3 mM
2	potassium phosphate pH 7.2	natural abundance		100 mM
3	H2O	natural abundance		90 %
4	D2O	natural abundance		10 %

4 3D HBHA(CO)NH

Instrument

Bruker DRX - 600 MHz with a z-axis gradient triple-resonance cryoprobe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293 (±0.1) K, pH 7.2 (±0.1), Details 0.15~0.3 mM Gb95 protein + pH7.2 100 mM potassium phosphate + 10% D2O

#	Name	Isotope labeling	Type	Concentration
1	Gb95	[U-100% 13C; U-100% 15N]		0.15-0.3 mM
2	potassium phosphate pH 7.2	natural abundance		100 mM
3	H2O	natural abundance		90 %
4	D2O	natural abundance		10 %

5 3D H(CCO)NH

Instrument

Bruker DRX - 600 MHz with a z-axis gradient triple-resonance cryoprobe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293 (±0.1) K, pH 7.2 (±0.1), Details 0.15~0.3 mM Gb95 protein + pH7.2 100 mM potassium phosphate + 10% D2O

#	Name	Isotope labeling	Type	Concentration
1	Gb95	[U-100% 13C; U-100% 15N]		0.15-0.3 mM
2	potassium phosphate pH 7.2	natural abundance		100 mM
3	H2O	natural abundance		90 %
4	D2O	natural abundance		10 %

6 3D C(CO)NH

Instrument

Bruker DRX - 600 MHz with a z-axis gradient triple-resonance cryoprobe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293 (±0.1) K, pH 7.2 (±0.1), Details 0.15~0.3 mM Gb95 protein + pH7.2 100 mM potassium phosphate + 10% D2O

#	Name	Isotope labeling	Type	Concentration
1	Gb95	[U-100% 13C; U-100% 15N]		0.15-0.3 mM
2	potassium phosphate pH 7.2	natural abundance		100 mM
3	H2O	natural abundance		90 %
4	D2O	natural abundance		10 %

7 3D HNCO

Instrument

Bruker DRX - 600 MHz with a z-axis gradient triple-resonance cryoprobe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293 (±0.1) K, pH 7.2 (±0.1), Details 0.15~0.3 mM Gb95 protein + pH7.2 100 mM potassium phosphate + 10% D2O

#	Name	Isotope labeling	Type	Concentration
1	Gb95	[U-100% 13C; U-100% 15N]		0.15-0.3 mM
2	potassium phosphate pH 7.2	natural abundance		100 mM
3	H2O	natural abundance		90 %
4	D2O	natural abundance		10 %

8 3D 1H-15N NOESY

Instrument

Bruker DRX - 600 MHz with a z-axis gradient triple-resonance cryoprobe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293 (±0.1) K, pH 7.2 (±0.1), Details 0.15~0.3 mM Gb95 protein + pH7.2 100 mM potassium phosphate + 10% D2O

#	Name	Isotope labeling	Type	Concentration
1	Gb95	[U-100% 13C; U-100% 15N]		0.15-0.3 mM
2	potassium phosphate pH 7.2	natural abundance		100 mM
3	H2O	natural abundance		90 %
4	D2O	natural abundance		10 %

9 3D 1H-13C NOESY(aliphatic)

Instrument

Bruker DRX - 600 MHz with a z-axis gradient triple-resonance cryoprobe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293 (±0.1) K, pH 7.2 (±0.1), Details 0.15~0.3 mM Gb95 protein + pH7.2 100 mM potassium phosphate + 10% D2O

#	Name	Isotope labeling	Type	Concentration
1	Gb95	[U-100% 13C; U-100% 15N]		0.15-0.3 mM
2	potassium phosphate pH 7.2	natural abundance		100 mM
3	H2O	natural abundance		90 %
4	D2O	natural abundance		10 %

10 3D 1H-13C NOESY(aromatic)

Instrument

Bruker DRX - 600 MHz with a z-axis gradient triple-resonance cryoprobe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293 (±0.1) K, pH 7.2 (±0.1), Details 0.15~0.3 mM Gb95 protein + pH7.2 100 mM potassium phosphate + 10% D2O

#	Name	Isotope labeling	Type	Concentration
1	Gb95	[U-100% 13C; U-100% 15N]		0.15-0.3 mM
2	potassium phosphate pH 7.2	natural abundance		100 mM
3	H2O	natural abundance		90 %
4	D2O	natural abundance		10 %

NMR combined restraints 5 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_16117_2kdm.nef
Input source #2: Coordindates	2kdm.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------
TTYKLILNLKQAKEEAIKEAVDAGTAEKYFKLIANAKTVEGVWTYKDEIKTFTVTE
||||||||||||||||||||||||||||||||||||||||||||||||||||||||
TTYKLILNLKQAKEEAIKEAVDAGTAEKYFKLIANAKTVEGVWTYKDEIKTFTVTE

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_16117_2kdm.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	593		100.0 (chain: A, length: 56)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	Warning	1262 (1)	noe	100.0 (chain: A, length: 56)
2	Distance restraints	CNS/XPLOR_distance_constraints_3	OK	63 (1)	hbond	66.1 (chain: A, length: 56)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_4	OK	74 (74)	.	85.7 (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: 292
  - ¹³C chemical shifts: 242
  - ¹⁵N chemical shifts: 59
- 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: 1245
- Weight of restraints: 1.0 (1245)
- Potential type of restraints: square-well-parabolic (1245)
- Range of distance target values: 2.4, 4.9 (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_3
  - 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_4
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 56, Sequence coverage: 85.7%
- Total number of restraints: 74
- Total number of restraints per polymer type: 74
- Weight of restraints: 1.0 (74)
- Potential type of restraints: square-well-parabolic (74)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords evolution, folding, nmr, protein design, protein structure, NMR