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BMRB: 16116

2KDL

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

Ga95

Entity

1. Ga95 (polymer, Thiol state: not present), 56 monomers, 6312.255 Da Detail

TTYKLILNLK QAKEEAIKEL VDAGTAEKYI KLIANAKTVE GVWTLKDEIK TFTVTE

Formula weight

6312.255 Da

Exptl. method

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 86.5 %, Completeness (bb): 96.7 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	86.5 % (585 of 676)	84.2 % (293 of 348)	86.9 % (233 of 268)	98.3 % (59 of 60)
Backbone	96.7 % (325 of 336)	94.7 % (108 of 114)	97.6 % (162 of 166)	98.2 % (55 of 56)
Sidechain	79.4 % (313 of 394)	79.1 % (185 of 234)	79.5 % (124 of 156)	100.0 % (4 of 4)
Aromatic	89.5 % (34 of 38)	94.7 % (18 of 19)	83.3 % (15 of 18)	100.0 % (1 of 1)
Methyl	68.2 % (60 of 88)	72.7 % (32 of 44)	63.6 % (28 of 44)

1. entity

TTYKLILNLK QAKEEAIKEL VDAGTAEKYI KLIANAKTVE GVWTLKDEIK TFTVTE

Show sample condition

Sample

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 288 (±0.1) K, pH 7.2 (±0.1), Details 0.15~0.3 mM Ga95 protein + pH7.2 100 mM potassium phosphate + 10% D2O

#	Name	Isotope labeling	Type	Concentration
1	Ga95	[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 %

Protein Blocks Logo

Calculated from 20 models in PDB: 2KDL, 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. Ga95, : 1 : 7 : 100 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 288 (±0.1) K, pH 7.2 (±0.1), Details 0.15~0.3 mM Ga95 protein + pH7.2 100 mM potassium phosphate + 10% D2O

#	Name	Isotope labeling	Type	Concentration
1	Ga95	[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 288 (±0.1) K, pH 7.2 (±0.1), Details 0.15~0.3 mM Ga95 protein + pH7.2 100 mM potassium phosphate + 10% D2O

#	Name	Isotope labeling	Type	Concentration
1	Ga95	[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 288 (±0.1) K, pH 7.2 (±0.1), Details 0.15~0.3 mM Ga95 protein + pH7.2 100 mM potassium phosphate + 10% D2O

#	Name	Isotope labeling	Type	Concentration
1	Ga95	[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 288 (±0.1) K, pH 7.2 (±0.1), Details 0.15~0.3 mM Ga95 protein + pH7.2 100 mM potassium phosphate + 10% D2O

#	Name	Isotope labeling	Type	Concentration
1	Ga95	[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 288 (±0.1) K, pH 7.2 (±0.1), Details 0.15~0.3 mM Ga95 protein + pH7.2 100 mM potassium phosphate + 10% D2O

#	Name	Isotope labeling	Type	Concentration
1	Ga95	[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 288 (±0.1) K, pH 7.2 (±0.1), Details 0.15~0.3 mM Ga95 protein + pH7.2 100 mM potassium phosphate + 10% D2O

#	Name	Isotope labeling	Type	Concentration
1	Ga95	[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 288 (±0.1) K, pH 7.2 (±0.1), Details 0.15~0.3 mM Ga95 protein + pH7.2 100 mM potassium phosphate + 10% D2O

#	Name	Isotope labeling	Type	Concentration
1	Ga95	[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 288 (±0.1) K, pH 7.2 (±0.1), Details 0.15~0.3 mM Ga95 protein + pH7.2 100 mM potassium phosphate + 10% D2O

#	Name	Isotope labeling	Type	Concentration
1	Ga95	[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 288 (±0.1) K, pH 7.2 (±0.1), Details 0.15~0.3 mM Ga95 protein + pH7.2 100 mM potassium phosphate + 10% D2O

#	Name	Isotope labeling	Type	Concentration
1	Ga95	[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 288 (±0.1) K, pH 7.2 (±0.1), Details 0.15~0.3 mM Ga95 protein + pH7.2 100 mM potassium phosphate + 10% D2O

#	Name	Isotope labeling	Type	Concentration
1	Ga95	[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 6 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_16116_2kdl.nef
Input source #2: Coordindates	2kdl.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------
TTYKLILNLKQAKEEAIKELVDAGTAEKYIKLIANAKTVEGVWTLKDEIKTFTVTE
||||||||||||||||||||||||||||||||||||||||||||||||||||||||
TTYKLILNLKQAKEEAIKELVDAGTAEKYIKLIANAKTVEGVWTLKDEIKTFTVTE

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_16116_2kdl.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	592		100.0 (chain: A, length: 56)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	OK	410 (1)	noe	98.2 (chain: A, length: 56)
2	Distance restraints	CNS/XPLOR_distance_constraints_5	OK	666 (1)	noe	96.4 (chain: A, length: 56)
3	Distance restraints	CNS/XPLOR_distance_constraints_3	OK	50 (1)	hbond	66.1 (chain: A, length: 56)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_4	OK	72 (72)	.	75.0 (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
  - ¹³C chemical shifts: 234
  - ¹H chemical shifts: 299
  - 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: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 56, Sequence coverage: 98.2%
- Total number of restraints: 410
- Weight of restraints: 1.0 (410)
- Potential type of restraints: square-well-parabolic (410)
- 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_5
  - Status: OK
  - Experiment type: noe
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 56, Sequence coverage: 96.4%
  - Total number of restraints: 657
  - Weight of restraints: 1.0 (657)
  - Potential type of restraints: square-well-parabolic (657)
  - 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: 50
    - Weight of restraints: 1.0 (50)
    - Potential type of restraints: square-well-parabolic (50)
    - Range of distance target values: 2.0, 2.75 (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: 75.0%
- Total number of restraints: 72
- Total number of restraints per polymer type: 72
- Weight of restraints: 1.0 (72)
- Potential type of restraints: square-well-parabolic (72)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

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