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- PDB-6onu: Complex structure of WhiB1 and region 4 of SigA in P21 space group. -

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Basic information

Entry
Database: PDB / ID: 6onu
TitleComplex structure of WhiB1 and region 4 of SigA in P21 space group.
Components
  • RNA polymerase sigma factor SigA
  • Transcriptional regulator WhiB1
KeywordsTRANSCRIPTION / Iron-sulfur cluster / transcription regulation / redox-sensing
Function / homology
Function and homology information


response to water / dinitrosyl-iron complex binding / protein-disulfide reductase (NAD(P)H) activity / response to nitric oxide / sigma factor activity / protein-disulfide reductase activity / peptidoglycan-based cell wall / cell redox homeostasis / DNA-templated transcription initiation / 4 iron, 4 sulfur cluster binding ...response to water / dinitrosyl-iron complex binding / protein-disulfide reductase (NAD(P)H) activity / response to nitric oxide / sigma factor activity / protein-disulfide reductase activity / peptidoglycan-based cell wall / cell redox homeostasis / DNA-templated transcription initiation / 4 iron, 4 sulfur cluster binding / negative regulation of DNA-templated transcription / DNA binding / metal ion binding / plasma membrane / cytoplasm
Similarity search - Function
Transcription factor WhiB / WhiB-like iron-sulfur binding domain / Transcription factor WhiB / 4Fe-4S WhiB-like (Wbl)-type iron-sulfur binding domain profile. / : / Sigma-70 factors family signature 1. / RNA polymerase sigma factor RpoD, C-terminal / RNA polymerase sigma factor RpoD / RNA polymerase sigma-70 region 1.2 / Sigma-70 factor, region 1.2 ...Transcription factor WhiB / WhiB-like iron-sulfur binding domain / Transcription factor WhiB / 4Fe-4S WhiB-like (Wbl)-type iron-sulfur binding domain profile. / : / Sigma-70 factors family signature 1. / RNA polymerase sigma factor RpoD, C-terminal / RNA polymerase sigma factor RpoD / RNA polymerase sigma-70 region 1.2 / Sigma-70 factor, region 1.2 / RNA polymerase sigma-70 region 3 / Sigma-70 region 3 / Sigma-70 factors family signature 2. / RNA polymerase sigma-70 / RNA polymerase sigma-70 region 4 / Sigma-70, region 4 / RNA polymerase sigma-70 region 2 / RNA polymerase sigma-70 like domain / Sigma-70 region 2 / RNA polymerase sigma factor, region 2 / RNA polymerase sigma factor, region 3/4-like / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / IRON/SULFUR CLUSTER / Transcriptional regulator WhiB1 / RNA polymerase sigma factor SigA
Similarity search - Component
Biological speciesMycobacterium tuberculosis H37Rv (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsWan, T. / Li, S.R. / Beltran, D.G. / Schacht, A. / Becker, D.C. / Zhang, L.M.
CitationJournal: Nucleic Acids Res. / Year: 2020
Title: Structural basis of non-canonical transcriptional regulation by the sigma A-bound iron-sulfur protein WhiB1 in M. tuberculosis.
Authors: Wan, T. / Li, S. / Beltran, D.G. / Schacht, A. / Zhang, L. / Becker, D.F. / Zhang, L.
History
DepositionApr 22, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 27, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 18, 2019Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 22, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.3Oct 11, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_conn_type / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.4Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Transcriptional regulator WhiB1
B: RNA polymerase sigma factor SigA
C: Transcriptional regulator WhiB1
D: RNA polymerase sigma factor SigA
E: Transcriptional regulator WhiB1
F: RNA polymerase sigma factor SigA
G: Transcriptional regulator WhiB1
H: RNA polymerase sigma factor SigA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,47313
Polymers88,9618
Non-polymers1,5135
Water5,531307
1
A: Transcriptional regulator WhiB1
B: RNA polymerase sigma factor SigA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,5923
Polymers22,2402
Non-polymers3521
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1670 Å2
ΔGint-28 kcal/mol
Surface area8540 Å2
MethodPISA
2
C: Transcriptional regulator WhiB1
D: RNA polymerase sigma factor SigA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,5923
Polymers22,2402
Non-polymers3521
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1670 Å2
ΔGint-30 kcal/mol
Surface area8430 Å2
MethodPISA
3
E: Transcriptional regulator WhiB1
F: RNA polymerase sigma factor SigA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,5923
Polymers22,2402
Non-polymers3521
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1700 Å2
ΔGint-27 kcal/mol
Surface area8400 Å2
MethodPISA
4
G: Transcriptional regulator WhiB1
H: RNA polymerase sigma factor SigA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,6984
Polymers22,2402
Non-polymers4582
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1740 Å2
ΔGint-27 kcal/mol
Surface area8360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.803, 144.439, 59.890
Angle α, β, γ (deg.)90.000, 106.761, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ASPASPARGARG(chain 'A' and (resid 2 through 4 or resid 6...AA2 - 42 - 4
12LYSLYSLYSLYS(chain 'A' and (resid 2 through 4 or resid 6...AA66
13CYSCYSPROPRO(chain 'A' and (resid 2 through 4 or resid 6...AA9 - 199 - 19
14GLYGLYGLYGLY(chain 'A' and (resid 2 through 4 or resid 6...AA21 - 6121 - 61
15SERSERLYSLYS(chain 'A' and (resid 2 through 4 or resid 6...AA64 - 7264 - 72
26ASPASPARGARG(chain 'E' and (resid 2 through 4 or resid 6...EE2 - 42 - 4
27LYSLYSLYSLYS(chain 'E' and (resid 2 through 4 or resid 6...EE66
28CYSCYSPROPRO(chain 'E' and (resid 2 through 4 or resid 6...EE9 - 199 - 19
29GLYGLYGLYGLY(chain 'E' and (resid 2 through 4 or resid 6...EE21 - 6121 - 61
210SERSERLYSLYS(chain 'E' and (resid 2 through 4 or resid 6...EE64 - 7264 - 72

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Components

#1: Protein
Transcriptional regulator WhiB1 / Iron-sulfur cluster protein WhiB1


Mass: 8553.324 Da / Num. of mol.: 4 / Fragment: UNP residues 1-76
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis H37Rv (bacteria)
Gene: whiB1, Rv3219 / Variant: ATCC 25618 / H37Rv / Production host: Escherichia coli (E. coli) / References: UniProt: P9WF43
#2: Protein
RNA polymerase sigma factor SigA / Sigma-A


Mass: 13686.857 Da / Num. of mol.: 4 / Fragment: region 4 (UNP residues 417-528)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis H37Rv (bacteria)
Gene: sigA, mysA, rpoD, rpoV, Rv2703, MTCY05A6.24 / Variant: ATCC 25618 / H37Rv / Production host: Escherichia coli (E. coli) / References: UniProt: P9WGI1
#3: Chemical
ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe4S4
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 307 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.24 Å3/Da / Density % sol: 45.2 % / Description: long brownish cuboid
Preparation: The protein was degraded in the crystal, resulting in a discrepancy between the Matthews coefficient and the reported protein sequence.
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 100 mM Bis-Tris, pH 5.5, 200 mM magnesium chloride, 25% PEG3350

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Data collection

DiffractionMean temperature: 100 K
Ambient temp details: Under continuous low-temperature nitrogen gas
Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9793 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 3, 2018 / Details: Mirror
RadiationMonochromator: Liquid nitrogen-cooled double crystal Si(111)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.85→50 Å / Num. obs: 55679 / % possible obs: 98.3 % / Redundancy: 14 % / Biso Wilson estimate: 35.5 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.061 / Net I/σ(I): 22.3
Reflection shellResolution: 1.85→1.87 Å / Redundancy: 14.4 % / Rmerge(I) obs: 1.42 / Num. unique obs: 2854 / CC1/2: 0.862 / % possible all: 98.3

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
PHENIX1.13_2998refinement
HKL-2000data reduction
HKL-2000data scaling
AutoSolphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 6ONO

6ono


Resolution: 1.85→36.87 Å / SU ML: 0.2351 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 27.9124 / Stereochemistry target values: GeoStd + Monomer Library
RfactorNum. reflection% reflectionSelection details
Rfree0.2354 2578 5.03 %Random selection
Rwork0.1942 48699 --
obs0.1964 51277 98.06 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 50.89 Å2
Refinement stepCycle: LAST / Resolution: 1.85→36.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4426 0 39 307 4772
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00914605
X-RAY DIFFRACTIONf_angle_d0.95996259
X-RAY DIFFRACTIONf_chiral_restr0.0567701
X-RAY DIFFRACTIONf_plane_restr0.0065818
X-RAY DIFFRACTIONf_dihedral_angle_d23.72441768
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.85-1.890.31841440.27782710X-RAY DIFFRACTION97.87
1.89-1.920.42441340.32332679X-RAY DIFFRACTION98.22
1.92-1.970.31641460.26562726X-RAY DIFFRACTION98.15
1.97-2.010.30611420.24952671X-RAY DIFFRACTION97.5
2.01-2.060.27651620.23192614X-RAY DIFFRACTION96.22
2.06-2.120.29591240.23342750X-RAY DIFFRACTION98.22
2.12-2.180.251510.21042687X-RAY DIFFRACTION98.54
2.18-2.250.26441230.22252745X-RAY DIFFRACTION98.66
2.25-2.330.27141300.20812704X-RAY DIFFRACTION97.93
2.33-2.420.23121490.19172716X-RAY DIFFRACTION99.27
2.42-2.530.27141440.20032693X-RAY DIFFRACTION96.43
2.53-2.670.24491380.20262696X-RAY DIFFRACTION98.51
2.67-2.840.26571640.2162691X-RAY DIFFRACTION98.72
2.84-3.050.24141580.21132731X-RAY DIFFRACTION99.28
3.05-3.360.26661210.20022703X-RAY DIFFRACTION96.78
3.36-3.850.20721690.18362721X-RAY DIFFRACTION99.14
3.85-4.840.19421440.15952694X-RAY DIFFRACTION97.43
4.84-36.880.20711350.17382768X-RAY DIFFRACTION98.31
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
14.23784609363-0.737274267542.53840808286.36606699853-0.291680018235.58618443216-0.0270511385794-0.0536550074110.121631747102-0.1863573635210.05640306729120.139405860145-0.6979034723220.0483685709585-0.06032483410490.377766375714-0.05867851663130.07857184324650.209676908764-0.06313581409640.276515544718-4.8767968770323.0131373464-10.8727425655
24.582532689763.547943367692.035545821597.104257556740.2161999607033.29251153524-0.05266668718590.1660009083020.0317036599967-0.02734629563950.305135409571-0.07899857219590.0528425521615-0.145173039419-0.2172213239080.2983607092820.02261986032580.03929590331810.2322065504140.004739676560260.245902130644-16.6678087947.65722570727-16.353419498
32.172855879180.3947459774580.4870929897555.558251637970.4322251688694.10349363709-0.08560701292680.1201990782710.199937254202-0.2515786166950.3223171463160.06725055999830.272218037737-0.177626268152-0.2142294932670.26106787725-0.0341471470595-0.01322393304670.2282716532240.1118323472980.256426040245-25.7636458981-12.3857421151-19.5447862453
43.38713152174-1.099595494331.003873891816.87569966162-3.668661672076.22996568604-0.2828505927390.0181773808095-0.0380510171362-0.535424692185-0.095171995831-0.4603649798330.4363003626060.2027282081090.2757288817320.3952395071240.008957883570260.1000714204520.2038126679640.03599171446850.359007210439-20.1386026699-28.9903031174-9.66677082856
57.310533545021.45688036299-1.522935241865.171647101431.198392120526.720321892510.384039641813-0.196414275258-0.243090208260.647815515703-0.1427387079920.2092544041-0.00307930964566-0.00241439458058-0.1930359454670.5520010103330.0136348499061-0.004537381266170.235707283373-0.001842365772410.345602156785-8.07563000767-28.4288139536-46.3223654637
65.83910564245-5.83078487287-1.833291772488.139632900940.2912275197962.35071148117-0.08277168256590.0389206111225-0.102193257788-0.3273341763380.3188546126910.1183949387860.15531404265-0.211608456346-0.2208801061860.71194579099-0.1516091917790.04626025621220.3825527133950.01661696717630.279529440084-18.4421153521-11.9877503926-40.2290179297
72.198929289520.810463525481-0.197833484415.72196798663-0.209816533234.877773897980.02786778894740.0783158478012-0.117323398449-0.6310995638890.4644972519020.2711318010580.0778623934637-0.509721183218-0.3907179322610.398586064092-0.0649718877228-0.001086729909330.3798713194950.2083585042080.383198171815-26.19530701648.97358930445-36.0762694333
86.806115341781.85655870278-3.163254490046.01425648584-3.200947596059.250060944030.0721812390927-0.0499847423736-0.3187418975590.1154323143420.03837913785890.0182951853239-0.3445043267320.232027688443-0.1048827397430.444412872879-0.0561188141914-0.03184522942570.2277257419870.03756268548550.299769781338-18.623388945324.1376256234-47.582394305
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain 'A' and resid 2 through 73)
2X-RAY DIFFRACTION2(chain 'B' and resid 455 through 523)
3X-RAY DIFFRACTION3(chain 'C' and resid 2 through 75)
4X-RAY DIFFRACTION4(chain 'D' and resid 455 through 522)
5X-RAY DIFFRACTION5(chain 'E' and resid 2 through 73)
6X-RAY DIFFRACTION6(chain 'F' and resid 454 through 521)
7X-RAY DIFFRACTION7(chain 'G' and resid 2 through 73)
8X-RAY DIFFRACTION8(chain 'H' and resid 456 through 520)

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