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- PDB-6ono: Complex structure of WhiB1 and region 4 of SigA in C2221 space group -

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Basic information

Entry
Database: PDB / ID: 6ono
TitleComplex structure of WhiB1 and region 4 of SigA in C2221 space group
Components
  • RNA polymerase sigma factor SigA
  • Transcription 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 / cell redox homeostasis / peptidoglycan-based cell wall / 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 / cell redox homeostasis / peptidoglycan-based cell wall / 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 / SAD / 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 4, 2019Group: Derived calculations / Category: pdbx_struct_assembly_gen / Item: _pdbx_struct_assembly_gen.asym_id_list
Revision 1.2Dec 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 1.3Jan 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 1.4Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_conn_type
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Transcription regulator WhiB1
B: RNA polymerase sigma factor SigA
C: Transcription regulator WhiB1
D: RNA polymerase sigma factor SigA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,3968
Polymers44,4804
Non-polymers9164
Water4,234235
1
A: Transcription regulator WhiB1
B: RNA polymerase sigma factor SigA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,8045
Polymers22,2402
Non-polymers5643
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1790 Å2
ΔGint-29 kcal/mol
Surface area8450 Å2
MethodPISA
2
C: Transcription 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 area1780 Å2
ΔGint-29 kcal/mol
Surface area8620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.445, 114.080, 144.713
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11D-606-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
12
22

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain 'B' and (resid 454 through 510 or resid 512...B2 - 42
121(chain 'B' and (resid 454 through 510 or resid 512...B44 - 47
131(chain 'B' and (resid 454 through 510 or resid 512...B49 - 56
141(chain 'B' and (resid 454 through 510 or resid 512...B58 - 61
151(chain 'B' and (resid 454 through 510 or resid 512...B64 - 73
261(chain 'D' and (resid 454 through 510 or resid 512...D2 - 42
271(chain 'D' and (resid 454 through 510 or resid 512...D44 - 47
281(chain 'D' and (resid 454 through 510 or resid 512...D49 - 56
291(chain 'D' and (resid 454 through 510 or resid 512...D58 - 61
2101(chain 'D' and (resid 454 through 510 or resid 512...D64 - 73
1112(chain 'A' and (resid 2 through 42 or resid 44...A454 - 510
1122(chain 'A' and (resid 2 through 42 or resid 44...A512 - 517
1132(chain 'A' and (resid 2 through 42 or resid 44...A519
1142(chain 'A' and (resid 2 through 42 or resid 44...A521 - 522
2152(chain 'C' and (resid 2 through 42 or resid 44...C454 - 510
2162(chain 'C' and (resid 2 through 42 or resid 44...C512 - 517
2172(chain 'C' and (resid 2 through 42 or resid 44...C519
2182(chain 'C' and (resid 2 through 42 or resid 44...C521 - 522

NCS ensembles :
ID
1
2

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Components

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


Mass: 8553.324 Da / Num. of mol.: 2 / 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.: 2 / 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.: 2 / Source method: obtained synthetically / Formula: Fe4S4
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 235 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 1.74 Å3/Da / Density % sol: 29.2 %
Description: long brownish cuboid shape, typical size is 0.2 mm * 0.2 mm * 0.4 mm
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5.5
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: Dec 2, 2017 / 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: 24510 / % possible obs: 91.5 % / Redundancy: 22.1 % / Biso Wilson estimate: 18.15 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.095 / Rpim(I) all: 0.018 / Rrim(I) all: 0.091 / Χ2: 1.117 / Net I/σ(I): 36.8
Reflection shellResolution: 1.85→1.88 Å / Redundancy: 13.2 % / Rmerge(I) obs: 0.894 / Mean I/σ(I) obs: 0.84 / Num. unique obs: 736 / CC1/2: 0.822 / Rpim(I) all: 0.258 / Rrim(I) all: 1.121 / Χ2: 0.819 / % possible all: 56.4

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
PHENIX1.13_2998refinement
HKL-2000data reduction
HKL-2000data scaling
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 1.85→44.79 Å / SU ML: 0.1834 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26.3013 / Stereochemistry target values: GeoStd + Monomer Library
RfactorNum. reflection% reflectionSelection details
Rfree0.237 972 4.81 %Random selection
Rwork0.1946 19246 --
obs0.1967 20218 75.3 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 33.64 Å2
Refinement stepCycle: LAST / Resolution: 1.85→44.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2247 0 30 235 2512
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00652352
X-RAY DIFFRACTIONf_angle_d0.87113194
X-RAY DIFFRACTIONf_chiral_restr0.0526359
X-RAY DIFFRACTIONf_plane_restr0.0051415
X-RAY DIFFRACTIONf_dihedral_angle_d21.8728910
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.85-1.950.3011470.2486866X-RAY DIFFRACTION24.26
1.95-2.070.3162700.26591443X-RAY DIFFRACTION39.94
2.07-2.230.26261200.22142458X-RAY DIFFRACTION68.09
2.23-2.460.23481370.21453403X-RAY DIFFRACTION93.58
2.46-2.820.24651690.21353632X-RAY DIFFRACTION99.63
2.82-3.550.2412090.19093656X-RAY DIFFRACTION99.64
3.55-44.810.21762200.16653788X-RAY DIFFRACTION99.55
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)
15.13051983107-2.21609909748-0.3115035906944.06652369678-0.9146387699385.330939085970.22306665755-0.02465768105340.2299173835710.253052146036-0.117929288839-0.182511909869-0.375015433571-0.039375218818-0.05113640119670.329213463231-0.0148325123787-0.0422159661840.1544106985390.05294690513430.06912912497622.306866506939.588178948798.1846908562
24.1046889771-1.376596360964.22771757572.04057737812-0.2835415954766.40129423423-0.0634400592887-0.08035120425950.1562728187170.172335710336-0.2264983254170.0691456161107-0.0300671920858-0.08001347513130.1911830392750.3568149477310.04528761778470.09499128183930.2113566087740.03663516706060.12650547896211.585497193345.256920841682.446750268
32.01576515155-0.411230237795-0.2830791518983.188005077280.4390519876515.5157528826-0.130203353068-0.0819319342333-0.02624715920230.0956143768159-0.1724005934860.2328820918430.06040169490510.03679730700980.09113504142690.219071092766-0.01920611006480.07461054453070.244246944723-0.1208518418050.112505041953.4393416486848.388407405862.0870398609
42.33157763685-1.55630363518-1.766311537724.266844443682.607888860195.28362184281-0.03801473664110.01362331484330.0148287326669-0.2145864708470.0196673593927-0.0245843735199-0.2606530307040.1182713778220.03440125904580.213951510524-0.07725691277070.05519154492750.218958227838-0.06024316193410.07217819460569.0023165874638.090120022445.7470992789
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 454 through 522)
3X-RAY DIFFRACTION3(chain 'C' and resid 2 through 75)
4X-RAY DIFFRACTION4(chain 'D' and resid 454 through 523)

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