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Found 1 Document (0.737 seconds)

BMRB: 17612

2LCH

Solution NMR Structure of a Protein With a Redesigned Hydrophobic Core, Northeast Structural Genomics Consortium Target OR38

Authors

Mills, J.L., Murphy, G., Miley, M., Machius, M., Kuhlman, B., Szyperski, T.

Assembly

OR38

Entity

1. OR38 (polymer, Thiol state: not present), 113 monomers, 13244.27 Da Detail

MGSHQEYIKK VTDELKELIQ NVNDDIKEVE KNPEDMEYWN KIYRLVHTMK EITETMGFSS VAKVLHTIMN LVDKMLNSEI KITSDLIDKV KKKLDMVTRE LDKKVSGSYL VPR

Formula weight

13244.27 Da

Exptl. method

solution NMR

Refine. method

simulated annealing, torsion angle dynamics, molecular dynamics

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 98.2 %, Completeness: 92.5 %, Completeness (bb): 95.5 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	92.5 % (1284 of 1388)	92.7 % (676 of 729)	91.3 % (492 of 539)	96.7 % (116 of 120)
Backbone	95.5 % (644 of 674)	94.7 % (215 of 227)	95.8 % (322 of 336)	96.4 % (107 of 111)
Sidechain	90.7 % (747 of 824)	91.8 % (461 of 502)	88.5 % (277 of 313)	100.0 % (9 of 9)
Aromatic	59.1 % (39 of 66)	66.7 % (22 of 33)	50.0 % (16 of 32)	100.0 % (1 of 1)
Methyl	89.0 % (121 of 136)	95.6 % (65 of 68)	82.4 % (56 of 68)

1. OR38

MGSHQEYIKK VTDELKELIQ NVNDDIKEVE KNPEDMEYWN KIYRLVHTMK EITETMGFSS VAKVLHTIMN LVDKMLNSEI KITSDLIDKV KKKLDMVTRE LDKKVSGSYL VPR

Show sample condition

Sample #1

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 1.0 mM [U-100% 13C; U-100% 15N] OR38, 95% H2O/5% D2O

#	Name	Isotope labeling	Concentration
1	OR38	[U-100% 13C; U-100% 15N]	1.0 mM
2	sodium phosphate	natural abundance	100 mM
3	sodium chloride	natural abundance	50 mM
4	H2O	natural abundance	95 %
5	D2O	natural abundance	5 %

Sample #2

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 1.0 mM [U-10% 13C; U-100% 15N] OR38, 95% H2O/5% D2O

#	Name	Isotope labeling	Concentration
6	OR38	[U-10% 13C; U-100% 15N]	1.0 mM
7	sodium phosphate	natural abundance	100 mM
8	sodium chloride	natural abundance	50 mM
9	H2O	natural abundance	95 %
10	D2O	natural abundance	5 %

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

Referencing offset: 0.06 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

Referencing offset: 0.06 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

Referencing offset: 0.04 ppm, Outliers: 1 Detail

LACS Plot; CO

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

Referencing offset: -0.09 ppm, Outliers: 1 Detail

Protein Blocks Logo

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

Release date

2011-05-31

Related entities 1. OR38, : 1 : 1 : 29 entities Detail

Experiments performed 11 experiments Detail

1 2D 1H-15N HSQC

Instrument

Varian INOVA - 750 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 1.0 mM [U-100% 13C; U-100% 15N] OR38, 95% H2O/5% D2O

#	Name	Isotope labeling	Concentration
1	OR38	[U-100% 13C; U-100% 15N]	1.0 mM
2	sodium phosphate	natural abundance	100 mM
3	sodium chloride	natural abundance	50 mM
4	H2O	natural abundance	95 %
5	D2O	natural abundance	5 %

2 2D 1H-13C HSQC

Instrument

Varian INOVA - 750 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 1.0 mM [U-100% 13C; U-100% 15N] OR38, 95% H2O/5% D2O

#	Name	Isotope labeling	Concentration
1	OR38	[U-100% 13C; U-100% 15N]	1.0 mM
2	sodium phosphate	natural abundance	100 mM
3	sodium chloride	natural abundance	50 mM
4	H2O	natural abundance	95 %
5	D2O	natural abundance	5 %

3 3D HNCO

Instrument

Varian INOVA - 750 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 1.0 mM [U-100% 13C; U-100% 15N] OR38, 95% H2O/5% D2O

#	Name	Isotope labeling	Concentration
1	OR38	[U-100% 13C; U-100% 15N]	1.0 mM
2	sodium phosphate	natural abundance	100 mM
3	sodium chloride	natural abundance	50 mM
4	H2O	natural abundance	95 %
5	D2O	natural abundance	5 %

4 3D CBCA(CO)NH

Instrument

Varian INOVA - 750 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 1.0 mM [U-100% 13C; U-100% 15N] OR38, 95% H2O/5% D2O

#	Name	Isotope labeling	Concentration
1	OR38	[U-100% 13C; U-100% 15N]	1.0 mM
2	sodium phosphate	natural abundance	100 mM
3	sodium chloride	natural abundance	50 mM
4	H2O	natural abundance	95 %
5	D2O	natural abundance	5 %

5 3D HNCACB

Instrument

Varian INOVA - 750 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 1.0 mM [U-100% 13C; U-100% 15N] OR38, 95% H2O/5% D2O

#	Name	Isotope labeling	Concentration
1	OR38	[U-100% 13C; U-100% 15N]	1.0 mM
2	sodium phosphate	natural abundance	100 mM
3	sodium chloride	natural abundance	50 mM
4	H2O	natural abundance	95 %
5	D2O	natural abundance	5 %

6 3D simutaneous 13C-aromatic,13C-aliphatic,15N edited 1H-1H NOESY

Instrument

Varian INOVA - 750 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 1.0 mM [U-100% 13C; U-100% 15N] OR38, 95% H2O/5% D2O

#	Name	Isotope labeling	Concentration
1	OR38	[U-100% 13C; U-100% 15N]	1.0 mM
2	sodium phosphate	natural abundance	100 mM
3	sodium chloride	natural abundance	50 mM
4	H2O	natural abundance	95 %
5	D2O	natural abundance	5 %

7 3D HBHA(CO)NH

Instrument

Varian INOVA - 750 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 1.0 mM [U-100% 13C; U-100% 15N] OR38, 95% H2O/5% D2O

#	Name	Isotope labeling	Concentration
1	OR38	[U-100% 13C; U-100% 15N]	1.0 mM
2	sodium phosphate	natural abundance	100 mM
3	sodium chloride	natural abundance	50 mM
4	H2O	natural abundance	95 %
5	D2O	natural abundance	5 %

8 3D HCCH-TOCSY

Instrument

Varian INOVA - 750 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 1.0 mM [U-100% 13C; U-100% 15N] OR38, 95% H2O/5% D2O

#	Name	Isotope labeling	Concentration
1	OR38	[U-100% 13C; U-100% 15N]	1.0 mM
2	sodium phosphate	natural abundance	100 mM
3	sodium chloride	natural abundance	50 mM
4	H2O	natural abundance	95 %
5	D2O	natural abundance	5 %

9 3D HCCH-COSY

Instrument

Varian INOVA - 750 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 1.0 mM [U-100% 13C; U-100% 15N] OR38, 95% H2O/5% D2O

#	Name	Isotope labeling	Concentration
1	OR38	[U-100% 13C; U-100% 15N]	1.0 mM
2	sodium phosphate	natural abundance	100 mM
3	sodium chloride	natural abundance	50 mM
4	H2O	natural abundance	95 %
5	D2O	natural abundance	5 %

10 2D 1H-15N HSQC

Instrument

Varian INOVA - 750 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 1.0 mM [U-10% 13C; U-100% 15N] OR38, 95% H2O/5% D2O

#	Name	Isotope labeling	Concentration
6	OR38	[U-10% 13C; U-100% 15N]	1.0 mM
7	sodium phosphate	natural abundance	100 mM
8	sodium chloride	natural abundance	50 mM
9	H2O	natural abundance	95 %
10	D2O	natural abundance	5 %

11 3D HN(CA)CO

Instrument

Varian INOVA - 750 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 1.0 mM [U-100% 13C; U-100% 15N] OR38, 95% H2O/5% D2O

#	Name	Isotope labeling	Concentration
1	OR38	[U-100% 13C; U-100% 15N]	1.0 mM
2	sodium phosphate	natural abundance	100 mM
3	sodium chloride	natural abundance	50 mM
4	H2O	natural abundance	95 %
5	D2O	natural abundance	5 %

NMR combined restraints 4 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_17612_2lch.nef
Input source #2: Coordindates	2lch.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
MGSHQEYIKKVTDELKELIQNVNDDIKEVEKNPEDMEYWNKIYRLVHTMKEITETMGFSSVAKVLHTIMNLVDKMLNSEIKITSDLIDKVKKKLDMVTRE
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
MGSHQEYIKKVTDELKELIQNVNDDIKEVEKNPEDMEYWNKIYRLVHTMKEITETMGFSSVAKVLHTIMNLVDKMLNSEIKITSDLIDKVKKKLDMVTRE

-------110---
LDKKVSGSYLVPR
|||||||||||||
LDKKVSGSYLVPR

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	113	0	0	100.0

Content subtype: combined_17612_2lch.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	1292		97.3 (chain: A, length: 113)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	OK	3180 (1)	noe	96.5 (chain: A, length: 113)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_3	OK	172 (172)	.	83.2 (chain: A, length: 113)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 113, Sequence coverage: 97.3%
- Total number of assignments
  - ¹H chemical shifts: 691
  - ¹³C chemical shifts: 489
  - ¹⁵N chemical shifts: 112
- 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

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	729	691	94.8
¹³C chemical shifts	539	489	90.7
¹⁵N chemical shifts	123	112	91.1

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	227	216	95.2
¹³C chemical shifts	226	215	95.1
¹⁵N chemical shifts	111	103	92.8

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	502	475	94.6
¹³C chemical shifts	313	274	87.5
¹⁵N chemical shifts	12	9	75.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	75	72	96.0
¹³C chemical shifts	75	59	78.7

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	33	25	75.8
¹³C chemical shifts	32	15	46.9
¹⁵N chemical shifts	1	1	100.0

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_2
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 113, Sequence coverage: 96.5%
- Total number of restraints: 3179
- Weight of restraints: 1.0 (3179)
- Potential type of restraints: square-well-parabolic (3179)
- Range of distance target values: 1.28, 3.0 (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: 113, Sequence coverage: 83.2%
- Total number of restraints: 172
- Total number of restraints per polymer type: 172
- Weight of restraints: 1.0 (172)
- Potential type of restraints: square-well-parabolic (172)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords NORTHEAST STRUCTURAL GENOMICS CONSORTIUM (NESG), Protein NMR, Protein Structure Initiative, PSI-2, Structural Genomics, Target OR38

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Found 1 Document (0.737 seconds)

BMRB: 17612

Sample #1

Sample #2

Chemical shift reference

Chemical shift reference

Chemical shift reference

Chemical shift reference

Related entities 1. OR38, : 1 : 1 : 29 entities Detail

Experiments performed 11 experiments Detail

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NMR combined restraints 4 contents Detail