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Found 1 Document (0.753 seconds)

BMRB: 18372

2LRH

SOLUTION NMR STRUCTURE OF DE NOVO DESIGNED PROTEIN, P-LOOP NTPASE FOLD, NORTHEAST STRUCTURAL GENOMICS CONSORTIUM TARGET OR137

Authors

Liu, G., Koga, N., Koga, R., Xiao, R., Lee, H., Janjua, H., Kohan, E., Acton, T.B., Everett, J.K., Baker, D., Montelione, G.T.

Assembly

OR137

Entity

1. OR137 (polymer, Thiol state: not present), 134 monomers, 16017.14 Da Detail

MKELILINTN NDELIKKIKK EVENQGYQVR DVNDSDELKK EMKKLAEEKN FEKILIISND KQLLKEMLEL ISKLGYKVFL LLQDQDENEL EEFKRKIESQ GYEVRKVTDD EEALKIVREF MQKAGSLEHH HHHH

Formula weight

16017.14 Da

Exptl. method

solution NMR

Refine. method

distance geometry, simulated annealing, molecular dynamics

Data set

assigned_chemical_shifts, RDCs

Chem. Shift Complete

Sequence coverage: 97.8 %, Completeness: 94.8 %, Completeness (bb): 95.1 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	94.8 % (1603 of 1691)	93.9 % (844 of 899)	96.0 % (617 of 643)	95.3 % (142 of 149)
Backbone	95.1 % (765 of 804)	93.0 % (253 of 272)	96.7 % (385 of 398)	94.8 % (127 of 134)
Sidechain	95.0 % (966 of 1017)	94.3 % (591 of 627)	96.0 % (360 of 375)	100.0 % (15 of 15)
Aromatic	76.1 % (67 of 88)	79.5 % (35 of 44)	72.7 % (32 of 44)
Methyl	98.6 % (144 of 146)	97.3 % (71 of 73)	100.0 % (73 of 73)

1. OR137

MKELILINTN NDELIKKIKK EVENQGYQVR DVNDSDELKK EMKKLAEEKN FEKILIISND KQLLKEMLEL ISKLGYKVFL LLQDQDENEL EEFKRKIESQ GYEVRKVTDD EEALKIVREF MQKAGSLEHH HHHH

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 1.19418 mM OR137.001, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
1	OR137.001	[U-100% 13C; U-100% 15N]	1.19418 mM
2	NaCl	natural abundance	100 mM
3	DTT	natural abundance	5 mM
4	NaN3	natural abundance	0.02 %
5	Tris-HCl pH 7.5	natural abundance	10 mM
6	H2O	natural abundance	90 %
7	D2O	natural abundance	10 %

Sample #2

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 1.19418 mM OR137.006, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
8	OR137.006	[U-5% 13C; U-100% 15N]	1.19418 mM
9	NaCl		100 mM
10	DTT		5 mM
11	NaN3		0.02 %
12	Tris-HCl pH 7.5		10 mM
13	H2O	natural abundance	90 %
14	D2O	natural abundance	10 %

Sample #3

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 1.19418 mM OR137.008, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
15	OR137.008	[U-5% 13C; U-100% 15N]	1.19418 mM
16	NaCl	natural abundance	100 mM
17	DTT	natural abundance	5 mM
18	NaN3	natural abundance	0.02 %
19	Tris-HCl pH 7.5	natural abundance	10 mM
20	H2O	natural abundance	90 %
21	D2O	natural abundance	10 %

LACS Plot; CA

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

Referencing offset: 0.09 ppm, Outliers: 2 Detail

LACS Plot; CB

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

Referencing offset: 0.09 ppm, Outliers: 2 Detail

LACS Plot; HA

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

Referencing offset: -0.08 ppm, Outliers: 1 Detail

LACS Plot; CO

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

Referencing offset: 0.29 ppm, Outliers: 1 Detail

Protein Blocks Logo

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

RDC

100 RDC values in 1 lists
Field strength (¹H) 599.520 MHz, Pressure 1 atm, Temperature 298 K, pH 6.5 Detail

Release date

2012-04-30

Related entities 1. OR137, : 1 : 2 : 14 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 1.19418 mM OR137.001, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
1	OR137.001	[U-100% 13C; U-100% 15N]	1.19418 mM
2	NaCl	natural abundance	100 mM
3	DTT	natural abundance	5 mM
4	NaN3	natural abundance	0.02 %
5	Tris-HCl pH 7.5	natural abundance	10 mM
6	H2O	natural abundance	90 %
7	D2O	natural abundance	10 %

2 2D 1H-13C 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 1.19418 mM OR137.001, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
1	OR137.001	[U-100% 13C; U-100% 15N]	1.19418 mM
2	NaCl	natural abundance	100 mM
3	DTT	natural abundance	5 mM
4	NaN3	natural abundance	0.02 %
5	Tris-HCl pH 7.5	natural abundance	10 mM
6	H2O	natural abundance	90 %
7	D2O	natural abundance	10 %

3 3D HNCO

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 1.19418 mM OR137.001, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
1	OR137.001	[U-100% 13C; U-100% 15N]	1.19418 mM
2	NaCl	natural abundance	100 mM
3	DTT	natural abundance	5 mM
4	NaN3	natural abundance	0.02 %
5	Tris-HCl pH 7.5	natural abundance	10 mM
6	H2O	natural abundance	90 %
7	D2O	natural abundance	10 %

4 3D CBCA(CO)NH

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 1.19418 mM OR137.001, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
1	OR137.001	[U-100% 13C; U-100% 15N]	1.19418 mM
2	NaCl	natural abundance	100 mM
3	DTT	natural abundance	5 mM
4	NaN3	natural abundance	0.02 %
5	Tris-HCl pH 7.5	natural abundance	10 mM
6	H2O	natural abundance	90 %
7	D2O	natural abundance	10 %

5 3D HNCACB

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 1.19418 mM OR137.001, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
1	OR137.001	[U-100% 13C; U-100% 15N]	1.19418 mM
2	NaCl	natural abundance	100 mM
3	DTT	natural abundance	5 mM
4	NaN3	natural abundance	0.02 %
5	Tris-HCl pH 7.5	natural abundance	10 mM
6	H2O	natural abundance	90 %
7	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 1.19418 mM OR137.001, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
1	OR137.001	[U-100% 13C; U-100% 15N]	1.19418 mM
2	NaCl	natural abundance	100 mM
3	DTT	natural abundance	5 mM
4	NaN3	natural abundance	0.02 %
5	Tris-HCl pH 7.5	natural abundance	10 mM
6	H2O	natural abundance	90 %
7	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 1.19418 mM OR137.001, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
1	OR137.001	[U-100% 13C; U-100% 15N]	1.19418 mM
2	NaCl	natural abundance	100 mM
3	DTT	natural abundance	5 mM
4	NaN3	natural abundance	0.02 %
5	Tris-HCl pH 7.5	natural abundance	10 mM
6	H2O	natural abundance	90 %
7	D2O	natural abundance	10 %

8 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 1.19418 mM OR137.006, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
8	OR137.006	[U-5% 13C; U-100% 15N]	1.19418 mM
9	NaCl		100 mM
10	DTT		5 mM
11	NaN3		0.02 %
12	Tris-HCl pH 7.5		10 mM
13	H2O	natural abundance	90 %
14	D2O	natural abundance	10 %

9 2D 1H-15N HSQC

Instrument

Varian INOVA - 600 MHz for RDC measurement

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 1.19418 mM OR137.008, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
15	OR137.008	[U-5% 13C; U-100% 15N]	1.19418 mM
16	NaCl	natural abundance	100 mM
17	DTT	natural abundance	5 mM
18	NaN3	natural abundance	0.02 %
19	Tris-HCl pH 7.5	natural abundance	10 mM
20	H2O	natural abundance	90 %
21	D2O	natural abundance	10 %

10 3D HCCH-TOCSY

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 1.19418 mM OR137.001, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
1	OR137.001	[U-100% 13C; U-100% 15N]	1.19418 mM
2	NaCl	natural abundance	100 mM
3	DTT	natural abundance	5 mM
4	NaN3	natural abundance	0.02 %
5	Tris-HCl pH 7.5	natural abundance	10 mM
6	H2O	natural abundance	90 %
7	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_18372_2lrh.nef
Input source #2: Coordindates	2lrh.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
MKELILINTNNDELIKKIKKEVENQGYQVRDVNDSDELKKEMKKLAEEKNFEKILIISNDKQLLKEMLELISKLGYKVFLLLQDQDENELEEFKRKIESQ
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
MKELILINTNNDELIKKIKKEVENQGYQVRDVNDSDELKKEMKKLAEEKNFEKILIISNDKQLLKEMLELISKLGYKVFLLLQDQDENELEEFKRKIESQ

-------110-------120-------130----
GYEVRKVTDDEEALKIVREFMQKAGSLEHHHHHH
||||||||||||||||||||||||||||||||||
GYEVRKVTDDEEALKIVREFMQKAGSLEHHHHHH

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	134	0	0	100.0

Content subtype: combined_18372_2lrh.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	1620		97.0 (chain: A, length: 134)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	Warning	6309 (1)	noe	96.3 (chain: A, length: 134)
2	Distance restraints	CNS/XPLOR_distance_constraints_3	OK	60 (1)	hbond	33.6 (chain: A, length: 134)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_4	OK	224 (224)	.	93.3 (chain: A, length: 134)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 134, Sequence coverage: 97.0%
- Total number of assignments
  - ¹H chemical shifts: 867
  - ¹³C chemical shifts: 612
  - ¹⁵N chemical shifts: 141
- 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

Comp_index_ID	Comp_ID	Atom_ID	CS value (ppm)
9	THR	HG1	6.143
58	SER	HG	5.021

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	899	865	96.2
¹³C chemical shifts	643	612	95.2
¹⁵N chemical shifts	153	141	92.2

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	272	261	96.0
¹³C chemical shifts	268	255	95.1
¹⁵N chemical shifts	134	126	94.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	627	604	96.3
¹³C chemical shifts	375	357	95.2
¹⁵N chemical shifts	19	15	78.9

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	77	77	100.0
¹³C chemical shifts	77	77	100.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	44	32	72.7
¹³C chemical shifts	44	31	70.5

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_2
- Status: Warning
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 134, Sequence coverage: 96.3%
- Total number of restraints: 6277
- Weight of restraints: 1.0 (6277)
- Potential type of restraints: square-well-parabolic (6277)
- Range of distance target values: 2.13, 4.46 (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: 134, Sequence coverage: 33.6%
  - Total number of restraints: 60
  - Weight of restraints: 1.0 (60)
  - Potential type of restraints: square-well-parabolic (60)
  - Range of distance target values: 1.99, 2.99 (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: 134, Sequence coverage: 93.3%
- Total number of restraints: 224
- Total number of restraints per polymer type: 224
- Weight of restraints: 1.0 (224)
- Potential type of restraints: square-well-parabolic (224)
- 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-Biology, Structural Genomics, Target OR137

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Found 1 Document (0.753 seconds)

BMRB: 18372

Sample #1

Sample #2

Sample #3

Chemical shift reference

Chemical shift reference

Chemical shift reference

Chemical shift reference

Related entities 1. OR137, : 1 : 2 : 14 entities Detail

Experiments performed 10 experiments Detail

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NMR combined restraints 5 contents Detail