BMRBj - BMREntryMaster

Found 1 Document (0.649 seconds)

BMRB: 34153

5OAY

M. tuberculosis [4Fe-4S] protein WhiB1 is a four-helix bundle that forms a NO-sensitive complex with sigmaA and regulates the major virulence factor ESX-1

Authors

Williamson, M.P., Green, J., Hounslow, A.M.

Assembly

Transcriptional regulator WhiB1

Entity

1. Transcriptional regulator WhiB1 (polymer), 94 monomers, 10369.56 Da Detail

AGENLYFQGA MDWRHKAVCR DEDPELFFPV GNSGPALAQI ADAKLVCNRC PVTTECLSWA LNTGQDSGVW GGMSEDERRA LKRRNARTKA RTGV

2. IRON/SULFUR CLUSTER (non-polymer), 351.640 Da

Total weight

10721.199 Da

Max. entity weight

10369.56 Da

Source organism

Mycobacterium tuberculosis H37Rv

Exptl. method

solution NMR

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 95.7 %, Completeness: 75.8 %, Completeness (bb): 89.0 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	75.8 % (794 of 1048)	69.2 % (378 of 546)	82.3 % (330 of 401)	85.1 % (86 of 101)
Backbone	89.0 % (495 of 556)	84.5 % (163 of 193)	91.2 % (249 of 273)	92.2 % (83 of 90)
Sidechain	64.5 % (372 of 577)	61.2 % (216 of 353)	71.8 % (153 of 213)	27.3 % (3 of 11)
Aromatic	71.8 % (56 of 78)	71.8 % (28 of 39)	69.4 % (25 of 36)	100.0 % (3 of 3)
Methyl	83.0 % (73 of 88)	81.8 % (36 of 44)	84.1 % (37 of 44)

1. Transcriptional regulator WhiB1

AGENLYFQGA MDWRHKAVCR DEDPELFFPV GNSGPALAQI ADAKLVCNRC PVTTECLSWA LNTGQDSGVW GGMSEDERRA LKRRNARTKA RTGV

Show sample condition

Sample

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0 (±0.05), Details 0.3 mM WhiB1 protein, 25 mM sodium phosphate, 250 mM sodium chloride, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
1	WhiB1 protein	natural abundance	0.3 mM
2	sodium chloride	natural abundance	250 mM
3	sodium phosphate	natural abundance	25 mM

LACS Plot; CA

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

Referencing offset: 0.05 ppm, Outliers: 3 Detail

LACS Plot; CB

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

Referencing offset: 0.05 ppm, Outliers: 3 Detail

LACS Plot; HA

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

Referencing offset: 0.03 ppm, Outliers: 1 Detail

LACS Plot; CO

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

Referencing offset: -0.37 ppm, Outliers: 3 Detail

Protein Blocks Logo

Calculated from 10 models in PDB: 5OAY, Strand ID: A Detail

Release date

2017-07-06

Citation

Structure of a Wbl protein and implications for NO sensing by M. tuberculosis
Kudhair, B.K., Hounslow, A.M., Rolfe, M.D., Crack, J.C., Hunt, D.M., Buxton, R.S., Smith, L.J., Le Brun, N.E., Williamson, M.P., Green, J.
Nat. Commun. (2017), 8, 2280-2280, PubMed 29273788 , DOI 10.1038/s41467-017-02418-y , Abstract

Related entities 1. Transcriptional regulator WhiB1, : 1 : 2 : 13 entities Detail

Experiments performed 10 experiments Detail

1 3D HNCO

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0 (±0.05), Details 0.3 mM WhiB1 protein, 25 mM sodium phosphate, 250 mM sodium chloride, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
1	WhiB1 protein	natural abundance	0.3 mM
2	sodium chloride	natural abundance	250 mM
3	sodium phosphate	natural abundance	25 mM

2 HN(CA)CO

Instrument

Bruker Avance - 800 MHz

Sample

#	Name	Isotope labeling	Concentration
1	WhiB1 protein	natural abundance	0.3 mM
2	sodium chloride	natural abundance	250 mM
3	sodium phosphate	natural abundance	25 mM

3 3D HNCA

Instrument

Bruker Avance - 800 MHz

Sample

#	Name	Isotope labeling	Concentration
1	WhiB1 protein	natural abundance	0.3 mM
2	sodium chloride	natural abundance	250 mM
3	sodium phosphate	natural abundance	25 mM

4 3D HN(CO)CA

Instrument

Bruker Avance - 800 MHz

Sample

#	Name	Isotope labeling	Concentration
1	WhiB1 protein	natural abundance	0.3 mM
2	sodium chloride	natural abundance	250 mM
3	sodium phosphate	natural abundance	25 mM

5 3D HNCACB

Instrument

Bruker Avance - 800 MHz

Sample

#	Name	Isotope labeling	Concentration
1	WhiB1 protein	natural abundance	0.3 mM
2	sodium chloride	natural abundance	250 mM
3	sodium phosphate	natural abundance	25 mM

6 HNCA(N)NH

Instrument

Bruker Avance - 800 MHz

Sample

#	Name	Isotope labeling	Concentration
1	WhiB1 protein	natural abundance	0.3 mM
2	sodium chloride	natural abundance	250 mM
3	sodium phosphate	natural abundance	25 mM

7 3D CBCA(CO)NH

Instrument

Bruker Avance - 800 MHz

Sample

#	Name	Isotope labeling	Concentration
1	WhiB1 protein	natural abundance	0.3 mM
2	sodium chloride	natural abundance	250 mM
3	sodium phosphate	natural abundance	25 mM

8 CCH-TOCSY

Instrument

Bruker Avance - 800 MHz

Sample

#	Name	Isotope labeling	Concentration
1	WhiB1 protein	natural abundance	0.3 mM
2	sodium chloride	natural abundance	250 mM
3	sodium phosphate	natural abundance	25 mM

9 3D HCCH-TOCSY

Instrument

Bruker Avance - 800 MHz

Sample

#	Name	Isotope labeling	Concentration
1	WhiB1 protein	natural abundance	0.3 mM
2	sodium chloride	natural abundance	250 mM
3	sodium phosphate	natural abundance	25 mM

10 HBCB(CGCD)HD

Instrument

Bruker Avance - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
1	WhiB1 protein	natural abundance	0.3 mM
2	sodium chloride	natural abundance	250 mM
3	sodium phosphate	natural abundance	25 mM

NMR combined restraints 5 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_34153_5oay.nef
Input source #2: Coordindates	5oay.cif
Diamagnetism of the molecular assembly	False (excluding Oxygen atoms)
Whether the assembly has a disulfide bond	None
Whether the assembly has a other bond	True (see coodinates for details)
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)

Ptnr_site_1	Ptnr_site_2	Redox_state_prediction_1	Redox_state_prediction_2	Distance (Å)
1:19:CYS:SG	2:1:SF4:FE3	unknown	unknown	n/a
1:47:CYS:SG	2:1:SF4:FE4	unknown	unknown	n/a
1:50:CYS:SG	2:1:SF4:FE1	unknown	unknown	n/a
1:56:CYS:SG	2:1:SF4:FE2	unknown	unknown	n/a

Non-standard residues

Chain_ID	Seq_ID	Comp_ID	Chem_comp_name	Experimental evidences
B	1	SF4	IRON/SULFUR CLUSTER	None

Sequence alignments

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

------------------10--------20--------30--------40--------50--------60--------70--------80----
AGENLYFQGAMDWRHKAVCRDEDPELFFPVGNSGPALAQIADAKLVCNRCPVTTECLSWALNTGQDSGVWGGMSEDERRALKRRNARTKARTGV
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
AGENLYFQGAMDWRHKAVCRDEDPELFFPVGNSGPALAQIADAKLVCNRCPVTTECLSWALNTGQDSGVWGGMSEDERRALKRRNARTKARTGV
--------10--------20--------30--------40--------50--------60--------70--------80--------90----

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	94	0	0	100.0

Content subtype: combined_34153_5oay.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Covalent bonds	assembly	OK	4		No information
1	Assigned chemical shifts	assigned_chemical_shifts_1	Warning	781		95.7 (chain: A, length: 94)
1	Distance restraints	CNS/XPLOR_distance_constraints_5	OK	250 (1)	noe	77.7 (chain: A, length: 94)
2	Distance restraints	CNS/XPLOR_distance_constraints_2	OK	34 (1)	hbond	53.2 (chain: A, length: 94)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_3	OK	158 (158)	.	80.9 (chain: A, length: 94)

Assigned chemical shifts

Saveframe: assigned_chemical_shifts_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 94, Sequence coverage: 95.7%
- Total number of assignments
  - ¹H chemical shifts: 373
  - ¹³C chemical shifts: 322
  - ¹⁵N chemical shifts: 86
- Completeness of assignments
  - Entity_assemble_ID: A
- Redox state of CYS
- 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	546	373	68.3
¹³C chemical shifts	401	322	80.3
¹⁵N chemical shifts	110	86	78.2

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	193	170	88.1
¹³C chemical shifts	188	177	94.1
¹⁵N chemical shifts	90	83	92.2

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	353	203	57.5
¹³C chemical shifts	213	145	68.1
¹⁵N chemical shifts	20	3	15.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	46	38	82.6
¹³C chemical shifts	46	38	82.6

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	39	28	71.8
¹³C chemical shifts	36	25	69.4
¹⁵N chemical shifts	3	3	100.0

Covalent bonds

Saveframe: assembly
- Status: OK

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_5
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 94, Sequence coverage: 77.7%
- Total number of restraints: 250
- Weight of restraints: 1.0 (250)
- Potential type of restraints: square-well-parabolic (250)
- Range of distance target values: 2.4, 3.65 (Å)
- Histogram of distance target values
- Distance restraints per residue
  - Chain_ID: A
  - Chain_ID: B
    None
- Distance restraints on contact map
- Saveframe: CNS/XPLOR_distance_constraints_2
  - Status: OK
  - Experiment type: hbond
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 94, Sequence coverage: 53.2%
  - Total number of restraints: 34
  - Weight of restraints: 1.0 (34)
  - Potential type of restraints: square-well-parabolic (34)
  - Range of distance target values: 2.9, 2.9 (Å)
  - Distance restraints per residue
    - Chain_ID: A
    - Chain_ID: B
      None
  - 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: 94, Sequence coverage: 80.9%
- Total number of restraints: 158
- Total number of restraints per polymer type: 158
- Weight of restraints: 1.0 (158)
- Potential type of restraints: square-well-parabolic (158)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords SIGNALING PROTEIN, Wbl protein, iron-sulfur, nitric oxide, sigmaA, tuberculosis

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Found 1 Document (0.649 seconds)

BMRB: 34153

Sample

Chemical shift reference

Chemical shift reference

Chemical shift reference

Chemical shift reference

Related entities 1. Transcriptional regulator WhiB1, : 1 : 2 : 13 entities Detail

Experiments performed 10 experiments Detail

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NMR combined restraints 5 contents Detail