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Found 1 Document (0.791 seconds)

BMRB: 16357

2KKE

Solution NMR Structure of a dimeric protein of unknown function from Methanobacterium thermoautotrophicum, Northeast Structural Genomics Consortium Target TR5

Authors

Swapna, G., Gunsalus, K., Huang, Y., Xiao, R., Everett, J.K., Acton, T.B., Montelione, G.T., NESG, N.

Assembly

TR5

Entity

1. TR5 (polymer, Thiol state: not present), 106 monomers, 11907.70 Da Detail

MVGRRPGGGL KDTKPVVVRL YPDEIEALKS RVPANTSMSA YIRRIILNHL EDEMVGRRPG GGLKDTKPVV VRLYPDEIEA LKSRVPANTS MSAYIRRIIL NHLEDE

Formula weight

11907.7 Da

Source organism

Methanothermobacter thermautotrophicus

Exptl. method

solution NMR

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 90.8 %, Completeness (bb): 91.6 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	90.8 % (1121 of 1234)	90.3 % (587 of 650)	90.0 % (434 of 482)	98.0 % (100 of 102)
Backbone	91.6 % (568 of 620)	94.3 % (200 of 212)	87.7 % (272 of 310)	98.0 % (96 of 98)
Sidechain	91.4 % (651 of 712)	88.4 % (387 of 438)	96.3 % (260 of 270)	100.0 % (4 of 4)
Aromatic	90.0 % (36 of 40)	90.0 % (18 of 20)	90.0 % (18 of 20)
Methyl	100.0 % (132 of 132)	100.0 % (66 of 66)	100.0 % (66 of 66)

1. TR5

MVGRRPGGGL KDTKPVVVRL YPDEIEALKS RVPANTSMSA YIRRIILNHL EDEMVGRRPG GGLKDTKPVV VRLYPDEIEA LKSRVPANTS MSAYIRRIIL NHLEDE

Show sample condition

Sample #1

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 303 K, pH 6.5, Details 0.4 mM TR5,25 mM Na2HPO4, 300 mM NaCl, 5% D2O, 1 x protease inhibitor (Roch). The His teg was removed by thrombin.

#	Name	Isotope labeling	Concentration
1	TR5-1	[U-100% 13C; U-100% 15N]	0.4 mM
2	Na2HPO4	natural abundance	25 mM
3	NaCl	natural abundance	300 mM
4	H2O	natural abundance	95 %
5	D2O	natural abundance	5 %

Sample #2

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 303 K, pH 6.5, Details 0.95 mM TR5,25 mM Na2HPO4, 300 mM NaCl, 5% D2O, 1 x protease inhibitor (Roch). The His teg was removed by thrombin.

#	Name	Isotope labeling	Concentration
6	TR5-2	[U-10% 13C; U-100% 15N]	0.95 mM
7	Na2HPO4	natural abundance	25 mM
8	NaCl	natural abundance	300 mM
9	H2O	natural abundance	95 %
10	D2O	natural abundance	5 %

Sample #3

#	Name	Isotope labeling	Concentration
11	TR5-3	[U-10% 13C; U-100% 15N] + unlabeled TR5 protein	0.4 mM
12	Na2HPO4	natural abundance	25 mM
13	NaCl	natural abundance	300 mM
14	H2O	natural abundance	95 %
15	D2O	natural abundance	5 %

LACS Plot; CA

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

Referencing offset: -0.33 ppm, Outliers: 2 Detail

LACS Plot; CB

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

Referencing offset: -0.33 ppm, Outliers: 2 Detail

LACS Plot; HA

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

Referencing offset: -0.06 ppm, Outliers: 2 Detail

LACS Plot; CO

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

Referencing offset: -0.12 ppm, Outliers: 4 Detail

Protein Blocks Logo

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

Release date

2009-07-06

Related entities 1. TR5, : 3 entities Detail

Experiments performed 13 experiments Detail

1 2D 1H-15N HSQC

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 303 K, pH 6.5, Details 0.4 mM TR5,25 mM Na2HPO4, 300 mM NaCl, 5% D2O, 1 x protease inhibitor (Roch). The His teg was removed by thrombin.

#	Name	Isotope labeling	Concentration
1	TR5-1	[U-100% 13C; U-100% 15N]	0.4 mM
2	Na2HPO4	natural abundance	25 mM
3	NaCl	natural abundance	300 mM
4	H2O	natural abundance	95 %
5	D2O	natural abundance	5 %

2 2D 1H-13C HSQC

Instrument

Varian INOVA - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
1	TR5-1	[U-100% 13C; U-100% 15N]	0.4 mM
2	Na2HPO4	natural abundance	25 mM
3	NaCl	natural abundance	300 mM
4	H2O	natural abundance	95 %
5	D2O	natural abundance	5 %

3 3D CBCA(CO)NH

Instrument

Varian INOVA - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
1	TR5-1	[U-100% 13C; U-100% 15N]	0.4 mM
2	Na2HPO4	natural abundance	25 mM
3	NaCl	natural abundance	300 mM
4	H2O	natural abundance	95 %
5	D2O	natural abundance	5 %

4 3D HNCACB

Instrument

Varian INOVA - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
1	TR5-1	[U-100% 13C; U-100% 15N]	0.4 mM
2	Na2HPO4	natural abundance	25 mM
3	NaCl	natural abundance	300 mM
4	H2O	natural abundance	95 %
5	D2O	natural abundance	5 %

5 3D HBHA(CO)NH

Instrument

Varian INOVA - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
1	TR5-1	[U-100% 13C; U-100% 15N]	0.4 mM
2	Na2HPO4	natural abundance	25 mM
3	NaCl	natural abundance	300 mM
4	H2O	natural abundance	95 %
5	D2O	natural abundance	5 %

6 3D HCCH-TOCSY

Instrument

Varian INOVA - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
1	TR5-1	[U-100% 13C; U-100% 15N]	0.4 mM
2	Na2HPO4	natural abundance	25 mM
3	NaCl	natural abundance	300 mM
4	H2O	natural abundance	95 %
5	D2O	natural abundance	5 %

7 3D HNCO

Instrument

Varian INOVA - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
1	TR5-1	[U-100% 13C; U-100% 15N]	0.4 mM
2	Na2HPO4	natural abundance	25 mM
3	NaCl	natural abundance	300 mM
4	H2O	natural abundance	95 %
5	D2O	natural abundance	5 %

8 3D 1H-13C NOESY

Instrument

Varian INOVA - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
1	TR5-1	[U-100% 13C; U-100% 15N]	0.4 mM
2	Na2HPO4	natural abundance	25 mM
3	NaCl	natural abundance	300 mM
4	H2O	natural abundance	95 %
5	D2O	natural abundance	5 %

9 3D 1H-15N NOESY

Instrument

Varian INOVA - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
1	TR5-1	[U-100% 13C; U-100% 15N]	0.4 mM
2	Na2HPO4	natural abundance	25 mM
3	NaCl	natural abundance	300 mM
4	H2O	natural abundance	95 %
5	D2O	natural abundance	5 %

10 3D- X-filtered NOESY

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 303 K, pH 6.5, Details 0.95 mM TR5,25 mM Na2HPO4, 300 mM NaCl, 5% D2O, 1 x protease inhibitor (Roch). The His teg was removed by thrombin.

#	Name	Isotope labeling	Concentration
11	TR5-3	[U-10% 13C; U-100% 15N] + unlabeled TR5 protein	0.4 mM
12	Na2HPO4	natural abundance	25 mM
13	NaCl	natural abundance	300 mM
14	H2O	natural abundance	95 %
15	D2O	natural abundance	5 %

11 2D 1H-15N HSQC

Instrument

Varian INOVA - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
6	TR5-2	[U-10% 13C; U-100% 15N]	0.95 mM
7	Na2HPO4	natural abundance	25 mM
8	NaCl	natural abundance	300 mM
9	H2O	natural abundance	95 %
10	D2O	natural abundance	5 %

12 2D 1H-13C HSQC

Instrument

Varian INOVA - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
6	TR5-2	[U-10% 13C; U-100% 15N]	0.95 mM
7	Na2HPO4	natural abundance	25 mM
8	NaCl	natural abundance	300 mM
9	H2O	natural abundance	95 %
10	D2O	natural abundance	5 %

13 2D HNOE

Instrument

Varian INOVA - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
6	TR5-2	[U-10% 13C; U-100% 15N]	0.95 mM
7	Na2HPO4	natural abundance	25 mM
8	NaCl	natural abundance	300 mM
9	H2O	natural abundance	95 %
10	D2O	natural abundance	5 %

NMR combined restraints 3 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints	combined_16357_2kke.nef
Input source #2: Coordindates	2kke.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	Error

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---
MVGRRPGGGLKDTKPVVVRLYPDEIEALKSRVPANTSMSAYIRRIILNHLEDE
|||||||||||||||||||||||||||||||||||||||||||||||||||||
MVGRRPGGGLKDTKPVVVRLYPDEIEALKSRVPANTSMSAYIRRIILNHLEDE

Entity_assembly_ID (NMR): B vs Auth_asym_ID (model): B

-------210-------220-------230-------240-------250---
MVGRRPGGGLKDTKPVVVRLYPDEIEALKSRVPANTSMSAYIRRIILNHLEDE
|||||||||||||||||||||||||||||||||||||||||||||||||||||
MVGRRPGGGLKDTKPVVVRLYPDEIEALKSRVPANTSMSAYIRRIILNHLEDE
--------10--------20--------30--------40--------50---

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	53	0	0	100.0
B	B	53	0	0	100.0

Content subtype: combined_16357_2kke.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Error	1121		No information
1	Distance restraints	CNS/XPLOR_distance_constraints_2	Warning	1969 (1)	noe	100.0 (chain: A, length: 53), 100.0 (chain: B, length: 53)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Error

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_2
- Status: Warning
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 53, Sequence coverage: 100.0%
  - Entity_assembly_ID: B, Chain length: 53, Sequence coverage: 100.0%
- Total number of restraints: 1968
- Weight of restraints: 1.0 (1968)
- Potential type of restraints: square-well-parabolic (1968)
- Range of distance target values: 3.02, 7.08 (Å)
- Histogram of distance target values
- Histogram of discrepancy in distance target values
- Distance restraints per residue
  - Chain_ID: A
  - Chain_ID: B
- Distance restraints on contact map

Keywords Methanothermobacter thermautotrophicus, NESG, O26567_METTH, Protein Structure Initiative, PSI-2, TR5, Northeast Structural Genomics Consortium, NORTHEAST STRUCTURAL GENOMICS CONSORTIUM (NESG), Protein NMR, Structural Genomics, Target TR5

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Found 1 Document (0.791 seconds)

BMRB: 16357

Sample #1

Sample #2

Sample #3

Chemical shift reference

Chemical shift reference

Chemical shift reference

Chemical shift reference

Related entities 1. TR5, : 3 entities Detail

Experiments performed 13 experiments Detail

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NMR combined restraints 3 contents Detail