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BMRB: 11590

2RV8

Solution Structure of the PhoP DNA-Binding Domain from Mycobacterium tuberculosis

Authors

Macdonald, R., Sarkar, D., Amer, B.R., Clubb, R.T.

Assembly

PhoP DNA-Binding Domain

Entity

1. PhoP DNA-Binding Domain (polymer, Thiol state: not present), 128 monomers, 14695.49 Da Detail

MGSSHHHHHH SSGLVPRGSH MKGNKEPRNV RLTFADIELD EETHEVWKAG QPVSLSPTEF TLLRYFVINA GTVLSKPKIL DHVWRYDFGG DVNVVESYVS YLRRKIDTGE KRLLHTLRGV GYVLREPR

Formula weight

14695.49 Da

Source organism

Mycobacterium tuberculosis

Exptl. method

solution NMR

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 88.3 %, Completeness: 75.5 %, Completeness (bb): 83.5 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	75.5 % (1140 of 1510)	72.0 % (565 of 785)	79.4 % (473 of 596)	79.1 % (102 of 129)
Backbone	83.5 % (631 of 756)	83.1 % (217 of 261)	84.2 % (314 of 373)	82.0 % (100 of 122)
Sidechain	70.1 % (611 of 871)	66.4 % (348 of 524)	76.8 % (261 of 340)	28.6 % (2 of 7)
Aromatic	36.8 % (53 of 144)	37.5 % (27 of 72)	34.3 % (24 of 70)	100.0 % (2 of 2)
Methyl	97.1 % (136 of 140)	97.1 % (68 of 70)	97.1 % (68 of 70)

1. PhoPC

MGSSHHHHHH SSGLVPRGSH MKGNKEPRNV RLTFADIELD EETHEVWKAG QPVSLSPTEF TLLRYFVINA GTVLSKPKIL DHVWRYDFGG DVNVVESYVS YLRRKIDTGE KRLLHTLRGV GYVLREPR

Show sample condition

Sample #1

Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	sodium phosphate	natural abundance	buffer	50.0 mM
2	sodium chloride	natural abundance	salt	300.0 mM
3	sodium azide	natural abundance		0.01 %
4	PhoPC	[U-100% 13C; U-100% 15N]	protein	1.0 (±0.5) mM
5	H2O	natural abundance	solvent	93 %
6	D2O	[U-2H]	solvent	7 %

Sample #2

Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
7	sodium phosphate	natural abundance	buffer	50.0 mM
8	sodium chloride	natural abundance	salt	300.0 mM
9	sodium azide	natural abundance		0.01 %
10	PhoPC	[U-100% 13C; U-100% 15N]	protein	1.0 (±0.5) mM
11	D2O	[U-2H]	solvent	100 %

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	external	direct	1.0
¹⁵N	liquid anhydrous ammonia	nitrogen	na	indirect	0.1013291

Referencing offset: 0.35 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	external	direct	1.0
¹⁵N	liquid anhydrous ammonia	nitrogen	na	indirect	0.1013291

Referencing offset: 0.35 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	external	direct	1.0
¹⁵N	liquid anhydrous ammonia	nitrogen	na	indirect	0.1013291

Referencing offset: 0.0 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	external	direct	1.0
¹⁵N	liquid anhydrous ammonia	nitrogen	na	indirect	0.1013291

Referencing offset: 0.32 ppm, Outliers: 2 Detail

Protein Blocks Logo

Calculated from 30 models in PDB: 2RV8, Strand ID: A Detail

Release date

2015-08-09

Citation

Solution structure of the PhoP DNA-binding domain from Mycobacterium tuberculosis
Macdonald, R., Sarkar, D., Amer, B.R., Clubb, R.T.
J. Biomol. NMR (2015), 63, 111-117, PubMed 26209027 , DOI 10.1007/s10858-015-9965-0 , Abstract

Related entities 1. PhoP DNA-Binding Domain, : 1 : 3 : 45 entities Detail

Experiments performed 20 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker Avence - 500 MHz

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	sodium phosphate	natural abundance	buffer	50.0 mM
2	sodium chloride	natural abundance	salt	300.0 mM
3	sodium azide	natural abundance		0.01 %
4	PhoPC	[U-100% 13C; U-100% 15N]	protein	1.0 (±0.5) mM
5	H2O	natural abundance	solvent	93 %
6	D2O	[U-2H]	solvent	7 %

2 2D 1H-13C HSQC aliphatic

Instrument

Bruker Avence - 800 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
7	sodium phosphate	natural abundance	buffer	50.0 mM
8	sodium chloride	natural abundance	salt	300.0 mM
9	sodium azide	natural abundance		0.01 %
10	PhoPC	[U-100% 13C; U-100% 15N]	protein	1.0 (±0.5) mM
11	D2O	[U-2H]	solvent	100 %

3 2D 1H-13C HSQC aromatic

Instrument

Bruker Avence - 500 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
7	sodium phosphate	natural abundance	buffer	50.0 mM
8	sodium chloride	natural abundance	salt	300.0 mM
9	sodium azide	natural abundance		0.01 %
10	PhoPC	[U-100% 13C; U-100% 15N]	protein	1.0 (±0.5) mM
11	D2O	[U-2H]	solvent	100 %

4 3D HNCO

Instrument

Bruker Avence - 500 MHz

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	sodium phosphate	natural abundance	buffer	50.0 mM
2	sodium chloride	natural abundance	salt	300.0 mM
3	sodium azide	natural abundance		0.01 %
4	PhoPC	[U-100% 13C; U-100% 15N]	protein	1.0 (±0.5) mM
5	H2O	natural abundance	solvent	93 %
6	D2O	[U-2H]	solvent	7 %

5 3D HNCACB

Instrument

Bruker Avence - 500 MHz

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	sodium phosphate	natural abundance	buffer	50.0 mM
2	sodium chloride	natural abundance	salt	300.0 mM
3	sodium azide	natural abundance		0.01 %
4	PhoPC	[U-100% 13C; U-100% 15N]	protein	1.0 (±0.5) mM
5	H2O	natural abundance	solvent	93 %
6	D2O	[U-2H]	solvent	7 %

6 3D CBCA(CO)NH

Instrument

Bruker Avence - 500 MHz

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	sodium phosphate	natural abundance	buffer	50.0 mM
2	sodium chloride	natural abundance	salt	300.0 mM
3	sodium azide	natural abundance		0.01 %
4	PhoPC	[U-100% 13C; U-100% 15N]	protein	1.0 (±0.5) mM
5	H2O	natural abundance	solvent	93 %
6	D2O	[U-2H]	solvent	7 %

7 3D HBHA(CO)NH

Instrument

Bruker Avence - 500 MHz

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	sodium phosphate	natural abundance	buffer	50.0 mM
2	sodium chloride	natural abundance	salt	300.0 mM
3	sodium azide	natural abundance		0.01 %
4	PhoPC	[U-100% 13C; U-100% 15N]	protein	1.0 (±0.5) mM
5	H2O	natural abundance	solvent	93 %
6	D2O	[U-2H]	solvent	7 %

8 3D HNHA

Instrument

Bruker Avence - 500 MHz

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	sodium phosphate	natural abundance	buffer	50.0 mM
2	sodium chloride	natural abundance	salt	300.0 mM
3	sodium azide	natural abundance		0.01 %
4	PhoPC	[U-100% 13C; U-100% 15N]	protein	1.0 (±0.5) mM
5	H2O	natural abundance	solvent	93 %
6	D2O	[U-2H]	solvent	7 %

9 3D 1H-15N NOESY

Instrument

Bruker Avence - 800 MHz

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	sodium phosphate	natural abundance	buffer	50.0 mM
2	sodium chloride	natural abundance	salt	300.0 mM
3	sodium azide	natural abundance		0.01 %
4	PhoPC	[U-100% 13C; U-100% 15N]	protein	1.0 (±0.5) mM
5	H2O	natural abundance	solvent	93 %
6	D2O	[U-2H]	solvent	7 %

10 3D 1H-15N TOCSY

Instrument

Bruker Avence - 800 MHz

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	sodium phosphate	natural abundance	buffer	50.0 mM
2	sodium chloride	natural abundance	salt	300.0 mM
3	sodium azide	natural abundance		0.01 %
4	PhoPC	[U-100% 13C; U-100% 15N]	protein	1.0 (±0.5) mM
5	H2O	natural abundance	solvent	93 %
6	D2O	[U-2H]	solvent	7 %

11 3D HNCA

Instrument

Bruker Avence - 600 MHz

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	sodium phosphate	natural abundance	buffer	50.0 mM
2	sodium chloride	natural abundance	salt	300.0 mM
3	sodium azide	natural abundance		0.01 %
4	PhoPC	[U-100% 13C; U-100% 15N]	protein	1.0 (±0.5) mM
5	H2O	natural abundance	solvent	93 %
6	D2O	[U-2H]	solvent	7 %

12 3D 1H-13C NOESY aliphatic

Instrument

Bruker Avence - 800 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
7	sodium phosphate	natural abundance	buffer	50.0 mM
8	sodium chloride	natural abundance	salt	300.0 mM
9	sodium azide	natural abundance		0.01 %
10	PhoPC	[U-100% 13C; U-100% 15N]	protein	1.0 (±0.5) mM
11	D2O	[U-2H]	solvent	100 %

13 3D 1H-13C NOESY aromatic

Instrument

Bruker Avence - 500 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
7	sodium phosphate	natural abundance	buffer	50.0 mM
8	sodium chloride	natural abundance	salt	300.0 mM
9	sodium azide	natural abundance		0.01 %
10	PhoPC	[U-100% 13C; U-100% 15N]	protein	1.0 (±0.5) mM
11	D2O	[U-2H]	solvent	100 %

14 3D HCCH-TOCSY

Instrument

Bruker Avence - 500 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
7	sodium phosphate	natural abundance	buffer	50.0 mM
8	sodium chloride	natural abundance	salt	300.0 mM
9	sodium azide	natural abundance		0.01 %
10	PhoPC	[U-100% 13C; U-100% 15N]	protein	1.0 (±0.5) mM
11	D2O	[U-2H]	solvent	100 %

15 3D C(CO)NH

Instrument

Bruker Avence - 500 MHz

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	sodium phosphate	natural abundance	buffer	50.0 mM
2	sodium chloride	natural abundance	salt	300.0 mM
3	sodium azide	natural abundance		0.01 %
4	PhoPC	[U-100% 13C; U-100% 15N]	protein	1.0 (±0.5) mM
5	H2O	natural abundance	solvent	93 %
6	D2O	[U-2H]	solvent	7 %

16 3D HCCH-COSY

Instrument

Bruker Avence - 500 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
7	sodium phosphate	natural abundance	buffer	50.0 mM
8	sodium chloride	natural abundance	salt	300.0 mM
9	sodium azide	natural abundance		0.01 %
10	PhoPC	[U-100% 13C; U-100% 15N]	protein	1.0 (±0.5) mM
11	D2O	[U-2H]	solvent	100 %

17 3D HN(CA)CO

Instrument

Bruker Avence - 800 MHz

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	sodium phosphate	natural abundance	buffer	50.0 mM
2	sodium chloride	natural abundance	salt	300.0 mM
3	sodium azide	natural abundance		0.01 %
4	PhoPC	[U-100% 13C; U-100% 15N]	protein	1.0 (±0.5) mM
5	H2O	natural abundance	solvent	93 %
6	D2O	[U-2H]	solvent	7 %

18 3D 1H-13C NOESY aliphatic

Instrument

Bruker Avence - 800 MHz

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	sodium phosphate	natural abundance	buffer	50.0 mM
2	sodium chloride	natural abundance	salt	300.0 mM
3	sodium azide	natural abundance		0.01 %
4	PhoPC	[U-100% 13C; U-100% 15N]	protein	1.0 (±0.5) mM
5	H2O	natural abundance	solvent	93 %
6	D2O	[U-2H]	solvent	7 %

19 3D HBHANH

Instrument

Bruker Avence - 600 MHz

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	sodium phosphate	natural abundance	buffer	50.0 mM
2	sodium chloride	natural abundance	salt	300.0 mM
3	sodium azide	natural abundance		0.01 %
4	PhoPC	[U-100% 13C; U-100% 15N]	protein	1.0 (±0.5) mM
5	H2O	natural abundance	solvent	93 %
6	D2O	[U-2H]	solvent	7 %

20 3D (H)CCH-TOCSY

Instrument

Bruker Avence - 800 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
7	sodium phosphate	natural abundance	buffer	50.0 mM
8	sodium chloride	natural abundance	salt	300.0 mM
9	sodium azide	natural abundance		0.01 %
10	PhoPC	[U-100% 13C; U-100% 15N]	protein	1.0 (±0.5) mM
11	D2O	[U-2H]	solvent	100 %

NMR combined restraints 4 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_11590_2rv8.nef
Input source #2: Coordindates	2rv8.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

120-----130-------140-------150-------160-------170-------180-------190-------200-------210-------22
MGSSHHHHHHSSGLVPRGSHMKGNKEPRNVRLTFADIELDEETHEVWKAGQPVSLSPTEFTLLRYFVINAGTVLSKPKILDHVWRYDFGGDVNVVESYVS
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
MGSSHHHHHHSSGLVPRGSHMKGNKEPRNVRLTFADIELDEETHEVWKAGQPVSLSPTEFTLLRYFVINAGTVLSKPKILDHVWRYDFGGDVNVVESYVS
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100

0-------230-------240-------
YLRRKIDTGEKRLLHTLRGVGYVLREPR
||||||||||||||||||||||||||||
YLRRKIDTGEKRLLHTLRGVGYVLREPR
-------110-------120--------

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	128	0	0	100.0

Content subtype: combined_11590_2rv8.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	1092		82.0 (chain: A, length: 128)
1	Distance restraints	CNS/XPLOR_distance_constraints_5	Warning	1449 (1)	noe	76.6 (chain: A, length: 128)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_2	OK	185 (185)	.	78.1 (chain: A, length: 128)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 128, Sequence coverage: 82.0%
- Total number of assignments
  - ¹H chemical shifts: 541
  - ¹³C chemical shifts: 453
  - ¹⁵N chemical shifts: 98
- 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	785	541	68.9
¹³C chemical shifts	596	453	76.0
¹⁵N chemical shifts	140	98	70.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	261	209	80.1
¹³C chemical shifts	256	204	79.7
¹⁵N chemical shifts	122	96	78.7

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	524	332	63.4
¹³C chemical shifts	340	249	73.2
¹⁵N chemical shifts	18	2	11.1

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	72	66	91.7
¹³C chemical shifts	72	66	91.7

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	72	28	38.9
¹³C chemical shifts	70	24	34.3
¹⁵N chemical shifts	2	2	100.0

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_5
- Status: Warning
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 128, Sequence coverage: 76.6%
- Total number of restraints: 1449
- Weight of restraints: 1.0 (1449)
- Potential type of restraints: square-well-parabolic (1449)
- Range of distance target values: 2.17, 3.9 (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: 128, Sequence coverage: 78.1%
- Total number of restraints: 185
- Total number of restraints per polymer type: 185
- Weight of restraints: 1.0 (185)
- Potential type of restraints: square-well-parabolic (185)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords MTB, NMR, PhoPC, heteronuclear NOE

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Found 1 Document (0.813 seconds)

BMRB: 11590

Sample #1

Sample #2

Chemical shift reference

Chemical shift reference

Chemical shift reference

Chemical shift reference

Related entities 1. PhoP DNA-Binding Domain, : 1 : 3 : 45 entities Detail

Experiments performed 20 experiments Detail

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NMR combined restraints 4 contents Detail