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BMRB: 16649

2KRU

Solution NMR structure of the PCP_red domain of light-independent protochlorophyllide reductase subunit B from Chlorobium tepidum. Northeast Structural Genomics Consortium Target CtR69A

Authors

He, Y., Eletsky, A., Lee, D., Ciccosanti, C., Janjua, H., Acton, T.B., Xiao, R., Everett, J.K., Montelione, G.T., Szyperski, T.

Assembly

CtR69A

Entity

1. CtR69A (polymer, Thiol state: not present), 63 monomers, 7301.244 Da Detail

MGELSWTAEA EKMLGKVPFF VRKKVRKNTD NYAREIGEPV VTADVFRKAK EHLGGLEHHH HHH

Formula weight

7301.244 Da

Source organism

Chlorobaculum tepidum

Exptl. method

Refine. method

simulated annealing

Data set

assigned_chemical_shifts, spectral_peak_list

Chem. Shift Complete

Sequence coverage: 87.3 %, Completeness: 83.7 %, Completeness (bb): 83.7 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	83.7 % (631 of 754)	83.8 % (330 of 394)	83.1 % (246 of 296)	85.9 % (55 of 64)
Backbone	83.7 % (313 of 374)	82.9 % (107 of 129)	83.7 % (154 of 184)	85.2 % (52 of 61)
Sidechain	84.0 % (368 of 438)	84.2 % (223 of 265)	83.5 % (142 of 170)	100.0 % (3 of 3)
Aromatic	53.8 % (42 of 78)	53.8 % (21 of 39)	52.6 % (20 of 38)	100.0 % (1 of 1)
Methyl	100.0 % (60 of 60)	100.0 % (30 of 30)	100.0 % (30 of 30)

1. CtR69A

MGELSWTAEA EKMLGKVPFF VRKKVRKNTD NYAREIGEPV VTADVFRKAK EHLGGLEHHH HHH

Show sample condition

Sample #1

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-100% 13C; U-100% 15N]		1.080 mM
2	MES	natural abundance		20 mM
3	sodium chloride	natural abundance		100 mM
4	calcium chloride	natural abundance		5 mM
5	NaN3	natural abundance		0.02 %

Sample #2

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
6	entity	[U-5% 13C; U-100% 15N]		0.986 mM
7	MES	natural abundance		20 mM
8	sodium chloride	natural abundance		100 mM
9	calcium chloride	natural abundance		5 mM
10	NaN3	natural abundance		0.02 %

Protein Blocks Logo

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

Release date

2010-02-21

Citation

Solution NMR structure of the PCP_red domain of light-independent protochlorophyllide reductase subunit B from Chlorobium tepidum. Northeast Structural Genomics Consortium Target CtR69A
He, Y., Eletsky, A., Lee, D., Ciccosanti, C., Janjua, H., Acton, T.B., Xiao, R., Everett, J.K., Montelione, G.T., Szyperski, T.
Not known

Related entities 1. CtR69A, : 1 : 1 : 69 entities Detail

Experiments performed 13 experiments Detail

1 2D 1H-15N HSQC

Instrument

Varian INOVA - 500 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-100% 13C; U-100% 15N]		1.080 mM
2	MES	natural abundance		20 mM
3	sodium chloride	natural abundance		100 mM
4	calcium chloride	natural abundance		5 mM
5	NaN3	natural abundance		0.02 %

2 2D 1H-13C CT-HSQC ali

Instrument

Varian INOVA - 500 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-100% 13C; U-100% 15N]		1.080 mM
2	MES	natural abundance		20 mM
3	sodium chloride	natural abundance		100 mM
4	calcium chloride	natural abundance		5 mM
5	NaN3	natural abundance		0.02 %

3 2D 1H-13C CT-HSQC (methyl)

Instrument

Varian INOVA - 500 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
6	entity	[U-5% 13C; U-100% 15N]		0.986 mM
7	MES	natural abundance		20 mM
8	sodium chloride	natural abundance		100 mM
9	calcium chloride	natural abundance		5 mM
10	NaN3	natural abundance		0.02 %

4 3D HNCO

Instrument

Varian INOVA - 500 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-100% 13C; U-100% 15N]		1.080 mM
2	MES	natural abundance		20 mM
3	sodium chloride	natural abundance		100 mM
4	calcium chloride	natural abundance		5 mM
5	NaN3	natural abundance		0.02 %

5 3D CBCA(CO)NH

Instrument

Varian INOVA - 500 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-100% 13C; U-100% 15N]		1.080 mM
2	MES	natural abundance		20 mM
3	sodium chloride	natural abundance		100 mM
4	calcium chloride	natural abundance		5 mM
5	NaN3	natural abundance		0.02 %

6 3D HNCACB

Instrument

Varian INOVA - 500 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-100% 13C; U-100% 15N]		1.080 mM
2	MES	natural abundance		20 mM
3	sodium chloride	natural abundance		100 mM
4	calcium chloride	natural abundance		5 mM
5	NaN3	natural abundance		0.02 %

7 3D HBHA(CO)NH

Instrument

Varian INOVA - 500 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-100% 13C; U-100% 15N]		1.080 mM
2	MES	natural abundance		20 mM
3	sodium chloride	natural abundance		100 mM
4	calcium chloride	natural abundance		5 mM
5	NaN3	natural abundance		0.02 %

8 3D HCCH-TOCSY

Instrument

Varian INOVA - 500 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-100% 13C; U-100% 15N]		1.080 mM
2	MES	natural abundance		20 mM
3	sodium chloride	natural abundance		100 mM
4	calcium chloride	natural abundance		5 mM
5	NaN3	natural abundance		0.02 %

9 3D HCCH-COSY ali

Instrument

Varian INOVA - 500 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-100% 13C; U-100% 15N]		1.080 mM
2	MES	natural abundance		20 mM
3	sodium chloride	natural abundance		100 mM
4	calcium chloride	natural abundance		5 mM
5	NaN3	natural abundance		0.02 %

10 13C/15N-NOESY

Instrument

Varian INOVA - 500 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-100% 13C; U-100% 15N]		1.080 mM
2	MES	natural abundance		20 mM
3	sodium chloride	natural abundance		100 mM
4	calcium chloride	natural abundance		5 mM
5	NaN3	natural abundance		0.02 %

11 2D 1H-13C CT-HSQC aro

Instrument

Varian INOVA - 500 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-100% 13C; U-100% 15N]		1.080 mM
2	MES	natural abundance		20 mM
3	sodium chloride	natural abundance		100 mM
4	calcium chloride	natural abundance		5 mM
5	NaN3	natural abundance		0.02 %

12 3D HCCH-COSY aro

Instrument

Varian INOVA - 500 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-100% 13C; U-100% 15N]		1.080 mM
2	MES	natural abundance		20 mM
3	sodium chloride	natural abundance		100 mM
4	calcium chloride	natural abundance		5 mM
5	NaN3	natural abundance		0.02 %

13 2D 1H-15N LR-HSQC (Histidine)

Instrument

Varian INOVA - 500 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-100% 13C; U-100% 15N]		1.080 mM
2	MES	natural abundance		20 mM
3	sodium chloride	natural abundance		100 mM
4	calcium chloride	natural abundance		5 mM
5	NaN3	natural abundance		0.02 %

NMR combined restraints 6 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_16649_2kru.nef
Input source #2: Coordindates	2kru.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---
MGELSWTAEAEKMLGKVPFFVRKKVRKNTDNYAREIGEPVVTADVFRKAKEHLGGLEHHHHHH
|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
MGELSWTAEAEKMLGKVPFFVRKKVRKNTDNYAREIGEPVVTADVFRKAKEHLGGLEHHHHHH

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	63	0	0	100.0

Content subtype: combined_16649_2kru.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	670		87.3 (chain: A, length: 63)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	OK	1323 (1)	noe	87.3 (chain: A, length: 63)
2	Distance restraints	DYANA/DIANA_distance_constraints_5	OK	1323 (1)	noe	87.3 (chain: A, length: 63)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_3	OK	70 (70)	.	65.1 (chain: A, length: 63)
2	Dihedral angle restraints	DYANA/DIANA_dihedral_4	OK	70 (70)	.	65.1 (chain: A, length: 63)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 63, Sequence coverage: 87.3%
- Total number of assignments
  - ¹H chemical shifts: 352
  - ¹³C chemical shifts: 255
  - ¹⁵N chemical shifts: 63
- 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

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_2
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 63, Sequence coverage: 87.3%
- Total number of restraints: 1323
- Weight of restraints: 1.0 (1323)
- Potential type of restraints: square-well-parabolic (1323)
- Range of distance target values: 1.57, 2.75 (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: DYANA/DIANA_distance_constraints_5
  - Status: OK
  - Experiment type: noe
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 63, Sequence coverage: 87.3%
  - Total number of restraints: 1323
  - Weight of restraints: 1.0 (1323)
  - Potential type of restraints: upper-bound-parabolic (1323)
  - Range of distance target values: 3.14, 5.5 (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: 63, Sequence coverage: 65.1%
- Total number of restraints: 70
- Total number of restraints per polymer type: 70
- Weight of restraints: 1.0 (70)
- Potential type of restraints: square-well-parabolic (70)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A
- Saveframe: DYANA/DIANA_dihedral_4
  - Status: OK
  - Experiment type: .
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 63, Sequence coverage: 65.1%
  - Total number of restraints: 70
  - Total number of restraints per polymer type: 70
  - Weight of restraints: 1.0 (70)
  - Potential type of restraints: square-well-parabolic (70)
  - Plot of Phi-Psi angle restraints
  - Dihedral angle restraints per residue
    - Chain_ID: A

Keywords NESG, PSI, bchB, protein structure, solution NMR