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Found 1 Document (0.668 seconds)

BMRB: 17390

2L82

Solution NMR Structure of de novo designed protein, P-loop NTPase fold, Northeast Structural Genomics Consortium Target OR32

Authors

Liu, G., Koga, N., Koga, R., Xiao, R., Hamilton, K., Janjua, H., Tong, S., Acton, T.B., Everett, J., Baker, D., Montelione, G.T.

Assembly

OR32

Entity

1. OR32 (polymer, Thiol state: not present), 162 monomers, 19663.73 Da Detail

MSQIFVVFSS DPEILKEIVR EIKRQGVRVV LLYSDQDEKR RRERLEEFEK QGVDVRTVED KEDFRENIRE IWERYPQLDV VVIVTTDDKE WIKDFIEEAK ERGVEVFVVY NNKDDDRRKE AQQEFRSDGV DVRTVSDKEE LIEQVRRFVR KVGSLEHHHH HH

Formula weight

19663.73 Da

Exptl. method

solution NMR

Refine. method

distance geometry, simulated annealing, molecular dynamics

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 96.9 %, Completeness: 90.1 %, Completeness (bb): 84.4 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	90.1 % (1796 of 1994)	95.3 % (1004 of 1053)	81.5 % (626 of 768)	96.0 % (166 of 173)
Backbone	84.4 % (817 of 968)	95.7 % (313 of 327)	73.0 % (351 of 481)	95.6 % (153 of 160)
Sidechain	95.6 % (1131 of 1183)	95.2 % (691 of 726)	96.2 % (427 of 444)	100.0 % (13 of 13)
Aromatic	87.5 % (133 of 152)	88.2 % (67 of 76)	86.5 % (64 of 74)	100.0 % (2 of 2)
Methyl	100.0 % (172 of 172)	100.0 % (86 of 86)	100.0 % (86 of 86)

1. OR32

MSQIFVVFSS DPEILKEIVR EIKRQGVRVV LLYSDQDEKR RRERLEEFEK QGVDVRTVED KEDFRENIRE IWERYPQLDV VVIVTTDDKE WIKDFIEEAK ERGVEVFVVY NNKDDDRRKE AQQEFRSDGV DVRTVSDKEE LIEQVRRFVR KVGSLEHHHH HH

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 1.06 mM [U-100% 13C; U-100% 15N] OR32, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
1	OR32	[U-100% 13C; U-100% 15N]	1.06 mM
2	H2O	natural abundance	90 %
3	D2O	natural abundance	10 %

Sample #2

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 0.85 mM [U-5% 13C; U-100% 15N] OR32, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
4	OR32	[U-5% 13C; U-100% 15N]	0.85 mM
5	H2O	natural abundance	90 %
6	D2O	natural abundance	10 %

LACS Plot; CA

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	null	indirect	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	null	indirect	0.1013291
³¹P	DSS	methyl protons	null	indirect	0.4048086

Referencing offset: 0.15 ppm, Outliers: 1 Detail

LACS Plot; CB

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	null	indirect	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	null	indirect	0.1013291
³¹P	DSS	methyl protons	null	indirect	0.4048086

Referencing offset: 0.15 ppm, Outliers: 1 Detail

LACS Plot; HA

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	null	indirect	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	null	indirect	0.1013291
³¹P	DSS	methyl protons	null	indirect	0.4048086

Referencing offset: -0.05 ppm, Outliers: 1 Detail

Protein Blocks Logo

Calculated from 20 models in PDB: 2L82, Strand ID: A Detail

Release date

2011-01-04

Citation

Role of backbone strain in de novo design of complex α/β protein structures
Koga, N., Koga, R., Liu, G., Castellanos, J., Montelione, G.T., Baker, D.
Nat. Commun. (2021), 12, 3921-3921, PubMed 34168113 , DOI 10.1038/s41467-021-24050-7 , Abstract

Related entities 1. OR32, : 1 : 6 entities Detail

Experiments performed 10 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 298 K, pH 6.5, Details 1.06 mM [U-100% 13C; U-100% 15N] OR32, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
1	OR32	[U-100% 13C; U-100% 15N]	1.06 mM
2	H2O	natural abundance	90 %
3	D2O	natural abundance	10 %

2 2D 1H-13C HSQC

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 0.85 mM [U-5% 13C; U-100% 15N] OR32, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
4	OR32	[U-5% 13C; U-100% 15N]	0.85 mM
5	H2O	natural abundance	90 %
6	D2O	natural abundance	10 %

3 3D HNCO

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 1.06 mM [U-100% 13C; U-100% 15N] OR32, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
1	OR32	[U-100% 13C; U-100% 15N]	1.06 mM
2	H2O	natural abundance	90 %
3	D2O	natural abundance	10 %

4 3D CBCA(CO)NH

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 1.06 mM [U-100% 13C; U-100% 15N] OR32, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
1	OR32	[U-100% 13C; U-100% 15N]	1.06 mM
2	H2O	natural abundance	90 %
3	D2O	natural abundance	10 %

5 3D HNCACB

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 1.06 mM [U-100% 13C; U-100% 15N] OR32, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
1	OR32	[U-100% 13C; U-100% 15N]	1.06 mM
2	H2O	natural abundance	90 %
3	D2O	natural abundance	10 %

6 3D 1H-13C arom NOESY

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 1.06 mM [U-100% 13C; U-100% 15N] OR32, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
1	OR32	[U-100% 13C; U-100% 15N]	1.06 mM
2	H2O	natural abundance	90 %
3	D2O	natural abundance	10 %

7 3D simutaneous 13C-aromatic,13C-aliphatic,15N edited 1H-1H NOESY

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 1.06 mM [U-100% 13C; U-100% 15N] OR32, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
1	OR32	[U-100% 13C; U-100% 15N]	1.06 mM
2	H2O	natural abundance	90 %
3	D2O	natural abundance	10 %

8 2D 1H-15N HSQC

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 0.85 mM [U-5% 13C; U-100% 15N] OR32, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
4	OR32	[U-5% 13C; U-100% 15N]	0.85 mM
5	H2O	natural abundance	90 %
6	D2O	natural abundance	10 %

9 3D HBHA(CO)NH

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 1.06 mM [U-100% 13C; U-100% 15N] OR32, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
1	OR32	[U-100% 13C; U-100% 15N]	1.06 mM
2	H2O	natural abundance	90 %
3	D2O	natural abundance	10 %

10 3D C(CO)NH

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 1.06 mM [U-100% 13C; U-100% 15N] OR32, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
1	OR32	[U-100% 13C; U-100% 15N]	1.06 mM
2	H2O	natural abundance	90 %
3	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_17390_2l82.nef
Input source #2: Coordindates	2l82.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
MSQIFVVFSSDPEILKEIVREIKRQGVRVVLLYSDQDEKRRRERLEEFEKQGVDVRTVEDKEDFRENIREIWERYPQLDVVVIVTTDDKEWIKDFIEEAK
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
MSQIFVVFSSDPEILKEIVREIKRQGVRVVLLYSDQDEKRRRERLEEFEKQGVDVRTVEDKEDFRENIREIWERYPQLDVVVIVTTDDKEWIKDFIEEAK

-------110-------120-------130-------140-------150-------160--
ERGVEVFVVYNNKDDDRRKEAQQEFRSDGVDVRTVSDKEELIEQVRRFVRKVGSLEHHHHHH
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
ERGVEVFVVYNNKDDDRRKEAQQEFRSDGVDVRTVSDKEELIEQVRRFVRKVGSLEHHHHHH

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	162	0	0	100.0

Content subtype: combined_17390_2l82.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	1766		96.9 (chain: A, length: 162)
1	Distance restraints	CNS/XPLOR_distance_constraints_3	OK	6153 (1)	noe	96.9 (chain: A, length: 162)
2	Distance restraints	CNS/XPLOR_distance_constraints_4	OK	82 (1)	hbond	42.0 (chain: A, length: 162)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_2	OK	240 (240)	.	88.3 (chain: A, length: 162)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 162, Sequence coverage: 96.9%
- Total number of assignments
  - ¹H chemical shifts: 1009
  - ¹³C chemical shifts: 584
  - ¹⁵N chemical shifts: 173
- Completeness of assignments
  - Entity_assemble_ID: A
- 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

Comp_index_ID	Comp_ID	Atom_ID	CS value (ppm)
9	SER	HG	5.912
34	SER	HG	5.08

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	1053	1007	95.6
¹³C chemical shifts	768	584	76.0
¹⁵N chemical shifts	192	173	90.1

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	327	315	96.3
¹³C chemical shifts	324	157	48.5
¹⁵N chemical shifts	160	153	95.6

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	726	692	95.3
¹³C chemical shifts	444	427	96.2
¹⁵N chemical shifts	32	20	62.5

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	87	86	98.9
¹³C chemical shifts	87	86	98.9

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	76	67	88.2
¹³C chemical shifts	74	64	86.5
¹⁵N chemical shifts	2	2	100.0

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_3
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 162, Sequence coverage: 96.9%
- Total number of restraints: 6153
- Weight of restraints: 1.0 (6153)
- Potential type of restraints: square-well-parabolic (6153)
- Range of distance target values: 2.15, 4.31 (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: 162, Sequence coverage: 42.0%
  - Total number of restraints: 82
  - Weight of restraints: 1.0 (82)
  - Potential type of restraints: square-well-parabolic (82)
  - Range of distance target values: 2.0, 2.55 (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_2
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 162, Sequence coverage: 88.3%
- Total number of restraints: 240
- Total number of restraints per polymer type: 240
- Weight of restraints: 1.0 (240)
- Potential type of restraints: square-well-parabolic (240)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords NORTHEAST STRUCTURAL GENOMICS CONSORTIUM (NESG), PSI-Biology, Protein NMR, Protein Structure Initiative, Structural Genomics, Target OR32

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Found 1 Document (0.668 seconds)

BMRB: 17390

Sample #1

Sample #2

Chemical shift reference

Chemical shift reference

Chemical shift reference

Related entities 1. OR32, : 1 : 6 entities Detail

Experiments performed 10 experiments Detail

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NMR combined restraints 5 contents Detail