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- PDB-8d5v: WhiB6 bound to the SigmaAr4-RNAP Beta flap tip chimera -

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Basic information

Entry
Database: PDB / ID: 8d5v
TitleWhiB6 bound to the SigmaAr4-RNAP Beta flap tip chimera
Components
  • Probable transcriptional regulator WhiB6
  • RNA polymerase sigma factor SigA,DNA-directed RNA polymerase subunit beta
KeywordsTRANSCRIPTION/Transferase / redox sensor / transcriptional factor / protein-DNA complex / TRANSCRIPTION / TRANSCRIPTION-Transferase complex
Function / homology
Function and homology information


response to water / Antimicrobial action and antimicrobial resistance in Mtb / dinitrosyl-iron complex binding / sigma factor activity / DNA-directed RNA polymerase complex / peptidoglycan-based cell wall / DNA-templated transcription initiation / ribonucleoside binding / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase ...response to water / Antimicrobial action and antimicrobial resistance in Mtb / dinitrosyl-iron complex binding / sigma factor activity / DNA-directed RNA polymerase complex / peptidoglycan-based cell wall / DNA-templated transcription initiation / ribonucleoside binding / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / 4 iron, 4 sulfur cluster binding / response to antibiotic / DNA-templated transcription / regulation of DNA-templated transcription / DNA binding / metal ion binding / plasma membrane / cytosol / 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 / RNA polymerase sigma-70 region 3 ...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 / DNA-directed RNA polymerase, beta subunit, external 1 domain superfamily / DNA-directed RNA polymerase, beta subunit, external 1 domain / RNA polymerase beta subunit external 1 domain / DNA-directed RNA polymerase beta subunit, bacterial-type / RNA polymerase Rpb2, domain 2 superfamily / RNA polymerase, beta subunit, protrusion / RNA polymerase beta subunit / RNA polymerase Rpb2, domain 2 / RNA polymerase Rpb2, domain 2 / RNA polymerase, beta subunit, conserved site / RNA polymerase Rpb2, domain 7 / RNA polymerase Rpb2, domain 3 / RNA polymerase Rpb2, OB-fold / RNA polymerase Rpb2, domain 7 / RNA polymerase Rpb2, domain 3 / RNA polymerases beta chain signature. / DNA-directed RNA polymerase, subunit 2, hybrid-binding domain / DNA-directed RNA polymerase, subunit 2 / DNA-directed RNA polymerase, subunit 2, hybrid-binding domain superfamily / RNA polymerase Rpb2, domain 6 / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
IRON/SULFUR CLUSTER / Probable transcriptional regulator WhiB6 / RNA polymerase sigma factor SigA / DNA-directed RNA polymerase subunit beta
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
Mycobacterium tuberculosis H37Rv (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsWan, T. / Zhang, L.M.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35 GM138157-01 United States
National Science Foundation (NSF, United States)CLP 1846908 United States
CitationJournal: To Be Published
Title: Crystal structure of WhiB6 and SigA4-betaTip complex
Authors: Wan, T. / Zhang, L.M.
History
DepositionJun 6, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 14, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Probable transcriptional regulator WhiB6
B: RNA polymerase sigma factor SigA,DNA-directed RNA polymerase subunit beta
C: Probable transcriptional regulator WhiB6
D: RNA polymerase sigma factor SigA,DNA-directed RNA polymerase subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,6196
Polymers50,9154
Non-polymers7032
Water2,468137
1
A: Probable transcriptional regulator WhiB6
B: RNA polymerase sigma factor SigA,DNA-directed RNA polymerase subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,8093
Polymers25,4582
Non-polymers3521
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1890 Å2
ΔGint-25 kcal/mol
Surface area9480 Å2
MethodPISA
2
C: Probable transcriptional regulator WhiB6
D: RNA polymerase sigma factor SigA,DNA-directed RNA polymerase subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,8093
Polymers25,4582
Non-polymers3521
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1750 Å2
ΔGint-26 kcal/mol
Surface area9480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.983, 66.540, 158.805
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
11A-334-

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 'A' and (resid 29 through 110 or resid 201))A29 - 110
211chain 'C'C29 - 110
112(chain 'B' and (resid 454 through 461 or resid 463 through 547))B454 - 461
122(chain 'B' and (resid 454 through 461 or resid 463 through 547))B463 - 547
212(chain 'D' and (resid 454 through 461 or resid 463 through 547))D454 - 461
222(chain 'D' and (resid 454 through 461 or resid 463 through 547))D463 - 547

NCS ensembles :
ID
1
2

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Components

#1: Protein Probable transcriptional regulator WhiB6


Mass: 12807.403 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: ATCC 25618 / H37Rv / Gene: whiB6, Rv3862c / Production host: Escherichia coli (E. coli) / References: UniProt: P9WF37
#2: Protein RNA polymerase sigma factor SigA,DNA-directed RNA polymerase subunit beta / Sigma-A / RNAP subunit beta / RNA polymerase subunit beta / Transcriptase subunit beta


Mass: 12650.234 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis H37Rv (bacteria), (gene. exp.) Mycobacterium tuberculosis (bacteria)
Strain: ATCC 25618 / H37Rv
Gene: sigA, mysA, rpoD, rpoV, Rv2703, MTCY05A6.24, rpoB, Rv0667, MTCI376.08c
Production host: Escherichia coli (E. coli)
References: UniProt: P9WGI1, UniProt: P9WGY9, DNA-directed RNA polymerase
#3: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER / Iron–sulfur cluster


Mass: 351.640 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe4S4 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 137 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 1.63 Å3/Da / Density % sol: 24.7 %
Description: long large rectangle crystals (0.1 mm X 0.2 mm X 0.4 mm)
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: 0.1 M Na Citrate pH 5.5, 20% PEG3000 / Temp details: 18 degree

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: Under liquid nitrogen stream / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 16, 2019
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 30736 / % possible obs: 97.44 % / Redundancy: 12.7 % / Biso Wilson estimate: 37.35 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.0672 / Rpim(I) all: 0.0198 / Rrim(I) all: 0.0702 / Net I/σ(I): 17.96
Reflection shellResolution: 1.8→1.864 Å / Redundancy: 13.6 % / Rmerge(I) obs: 1.59 / Mean I/σ(I) obs: 1.51 / Num. unique obs: 3011 / CC1/2: 0.809 / CC star: 0.946 / Rpim(I) all: 0.4418 / Rrim(I) all: 1.652 / % possible all: 97.53

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Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6ONO

6ono


Resolution: 1.8→33.27 Å / SU ML: 0.2669 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 28.8498
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2306 1560 5.1 %
Rwork0.2102 29004 -
obs0.2112 30564 97.46 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 54.29 Å2
Refinement stepCycle: LAST / Resolution: 1.8→33.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2795 0 16 137 2948
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00992866
X-RAY DIFFRACTIONf_angle_d1.19333889
X-RAY DIFFRACTIONf_chiral_restr0.0746433
X-RAY DIFFRACTIONf_plane_restr0.0074512
X-RAY DIFFRACTIONf_dihedral_angle_d25.87821094
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.860.34821280.32782623X-RAY DIFFRACTION97.59
1.86-1.920.35671290.37892548X-RAY DIFFRACTION95.68
1.92-20.35481640.31242562X-RAY DIFFRACTION96.53
2-2.090.36321480.31742546X-RAY DIFFRACTION94.99
2.09-2.20.32571370.26582609X-RAY DIFFRACTION98.35
2.2-2.340.31461430.25742629X-RAY DIFFRACTION98.12
2.34-2.520.26961460.24262634X-RAY DIFFRACTION97.78
2.52-2.780.2841580.23742655X-RAY DIFFRACTION98.77
2.78-3.180.23271220.23212718X-RAY DIFFRACTION98.99
3.18-40.22291160.18492713X-RAY DIFFRACTION97.99
4-33.270.17011690.16452767X-RAY DIFFRACTION97.44
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)
14.339081024920.1619563754880.1686675922358.31114765501-1.17766466457.82143574529-0.1861851181650.350336664072-0.253970286661-0.3124307731010.2102826872590.6926561574660.536028321818-1.35597049201-0.0174903657720.42641946768-0.0862388633401-0.01479477023180.413621666662-0.08855449487820.4383799017379.44842593684-2.3205565193530.2192516252
23.31702381641-0.4547376073291.141853812396.16995246713-0.7086856188178.04190586168-0.0625316664580.0884168260618-0.09608607787460.000483895963067-0.01139584694480.217989749490.0137384321266-0.3348610777620.04397518020420.247965706092-0.03222593805020.0402357333360.290694355834-0.05413526078440.31920166225214.21358546640.76750964923238.2868138616
33.324061743170.467496321079-0.1331545701327.01684532865-1.170051067338.78555715398-0.126679793117-0.240931786118-0.2622280531280.8493004985850.123360908258-0.3273536483090.1377288512890.3122570254160.04970620779570.351789425732-0.0117260234789-0.03397072978540.270426459904-0.03525929258630.31490544371820.3516042359-0.45947545279747.2056619604
47.506457591981.70393599926-0.03569600148565.04734011327-2.687650234725.26764967425-0.1202012896920.758893667237-0.858709349334-0.6349102923350.5126753082760.2480042785810.73737421377-0.149905285226-0.09509518517480.3774191988180.00319095392645-0.01518503839890.359611712873-0.06152711118860.46442695201914.5034736153-17.515132186723.5878258982
59.144040436580.6779755000420.8215483659934.05612327432-0.9646301662895.391116550290.01594183705270.9124631221350.44552697867-0.179641975019-0.298207497618-0.0508593008414-0.373142803090.1895314068570.1189131592390.453624298768-0.007772983190260.1078920552260.440377208673-0.03044897046110.46697588729125.242548024-9.3199170338819.2408659376
65.714807559981.536470293530.5289333703143.29290953687-0.07633182034263.48315466664-0.25250325661.81802951679-1.92245373268-0.468628538070.327501734785-0.09057008423110.8747828746440.6647978816970.1549776916630.6309255432010.1048547329020.1852084783510.584221978047-0.09356337949570.79262379096631.426429107-18.168162268918.4659183114
76.765991358532.881833366730.4861136949312.42113292197-0.385344018594.09509682439-0.8859727194161.494522677180.795751799636-0.6527330785280.129028199716-1.102123329540.2272793308952.037065446470.2385470189210.537393329244-0.05946508661530.1405539625740.8763006730820.1121165681410.60742032400235.4740784519-6.878086273515.2952126189
87.826138562451.79237062006-0.5379440558253.34386104499-1.422894435315.368389789350.2722674719060.248213206331.562938893220.0771340670364-0.011046804085-0.104337508614-0.4492900898010.5490197897560.1770970680360.399770768373-0.03342647709340.06865904506020.376181784464-0.01120457184940.68795289801328.946145796-3.4507785232525.241237128
96.968856030681.378821328910.6896660484995.19242987682-1.672504678134.449502369550.268670797341-0.467489030163-0.02953140929970.953698318215-0.6567336647820.641071676178-0.417552375517-1.02934971666-0.0863567617220.320621432888-0.007988467984430.03005689678840.417239912236-0.09134273614070.4785514037814.1960265022-8.2613332857831.8086601126
109.256567524691.880962452941.256209163335.43869519863-1.934257193725.91136006010.544094736344-0.823707349275-0.8983310957960.342874806649-0.354027692863-0.2672758930180.103779971539-0.336795498846-0.04280196609870.338001044137-0.1182703122980.03134299365170.3987348854940.0008718319471280.46939527941519.9672289308-21.502738697433.6664082604
119.42568771541.520699529750.6920729611865.43093147794-1.100306684756.806442555650.220587392551-0.405288964993-0.43653151831-0.177914430761-0.264314938185-0.6954733433260.3584331905951.133999409660.06379891561680.396016923275-0.02806033988210.1082087156370.4683164476340.0278703014390.56075029775125.5174899396-17.004712742932.6699808672
126.914957392120.8225297550590.4699826526616.03008210821-0.2003618388257.409368766090.3581959694-0.6293908627672.284233796871.18630010913-0.1448419500380.87543620293-2.3018133634-0.904494332915-0.1408117918680.9407962396980.3117454020930.01172575915850.599332944481-0.09841990549120.8118027148119.32331110126.89930440274.17417200485
136.525270132331.116666142680.0413832235436.57218561201-0.1421820647889.55845103430.01458584499650.0927629054220.858247676163-0.2485566860450.2978951828620.133192609059-0.779122965213-0.80557803664-0.1813005907990.5940676579680.000165133252012-0.1023706798180.5265196937680.1264449614090.37655125180319.807950597720.3570243292-3.80638421831
142.172298256620.3105942448771.013057864548.173751838440.9971582310489.131192316710.109258694428-1.62316782327-0.3613638015250.8683083174790.1506589258420.8417560674741.07510105876-1.89480890524-0.143583651350.506386772049-0.0920967097626-0.07076468022330.8063882750270.08728874735470.40549628646716.601141163314.41884070894.75269153915
156.76433399483-0.666411787171-0.8435425747444.77039834611.645201007429.788171074570.231714887236-0.0798735119695-0.6821139706630.166296042844-0.093751070716-0.1170114881880.97136166204-0.516719746967-0.3217554786640.546752339417-0.113547384089-0.1999933582350.4082052596160.0547615955260.4627108681520.74979465768.24070868089-4.13013603939
166.9000933981-1.01430687256-2.89464902834.42965847564-0.8937101207119.483415598590.934465426486-0.8776568253941.46547776880.131359820149-0.101403767473-1.26899600562-1.461852559171.81621774131-0.4224923829690.715469562208-0.1620748704870.1626597688770.577010945738-0.1031291669860.64334159674334.505668693327.574566954314.0576785566
176.90419000303-1.1111605672-2.648100275834.35383723905-0.8947244966712.270390219180.2601935388180.07630512475180.548864362748-0.1334311647280.115345851610.0424760309827-0.4853627973360.328695170024-0.2489783833030.463274156583-0.01974079080620.03010823993740.351857770853-0.04820268566880.40770346013326.228571620821.772242822222.3377366837
183.614079874230.122040141577-3.467857752684.905427635210.3649060109245.395060914130.150940514425-2.36524964450.04510413419490.9771794410440.156353848976-1.42704101098-0.4287795630353.027321507860.1961179846240.422487131715-0.0072660390489-0.01204758095250.930677022739-0.08216198798930.67564595612134.776441299317.378167605527.4491698345
197.04981332437-0.0322709294712-2.347990044774.95077221134-0.1651627942282.29758910479-0.526338406141-0.809522418242-0.5613939772450.5731146606810.6551903914360.01425262035230.3845421733950.145988356077-0.1053395714260.4631663681790.09885083096850.0663685970310.3764369274920.01533974258450.45755917728222.673356772516.818577259931.4614337123
204.25741915486-0.405486301333-2.866802217963.62918726019-1.46312197322.806683205490.06689990281750.073402705739-0.5638326329150.0003475832417830.1682253334520.340213361810.551722993626-0.396176659408-0.02805964951990.3665363859580.00196811372225-0.02396418354240.43772971939-0.02634617766960.48799479766120.4020398715.234296664119.3346857679
217.1174527637-1.06159516603-1.684606449574.24158345915-0.1551812963928.597499501270.1711422596490.428006587729-0.0703040293946-0.630552797606-0.449154450698-0.708078416087-0.4685703975681.0954878201-0.1847445449530.5529936889750.05116701175150.1208434301810.6046921398110.08982939758520.410128106632.501056046420.64911593676.17620560327
225.03844854791-1.41857373342-1.27311348731.60067410817-0.5228515540171.0260386665-0.345639863627-0.7159768917130.0128971858205-0.420720137269-0.119951875073-0.7607604182220.9305174897322.690368496980.1695085038820.6692053306290.212697740946-0.0541333157481.486876378140.1844408671930.91837274647742.96992533914.125278945314.843075163
233.48665292022-1.30494424739-1.804819836835.13848955566-0.3721297575737.661037301030.343832982990.685314134087-0.693249974863-0.722523338429-0.140595180132-1.044943681560.8984558062991.61485517173-0.02131171916920.4912384418250.07401576205580.04185237782690.626736484158-0.0906207042350.56328373012234.892588799113.871941768113.4907018176
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 28 through 46 )
2X-RAY DIFFRACTION2chain 'A' and (resid 47 through 84 )
3X-RAY DIFFRACTION3chain 'A' and (resid 85 through 111 )
4X-RAY DIFFRACTION4chain 'B' and (resid 453 through 466 )
5X-RAY DIFFRACTION5chain 'B' and (resid 467 through 479 )
6X-RAY DIFFRACTION6chain 'B' and (resid 480 through 488 )
7X-RAY DIFFRACTION7chain 'B' and (resid 489 through 499 )
8X-RAY DIFFRACTION8chain 'B' and (resid 500 through 515 )
9X-RAY DIFFRACTION9chain 'B' and (resid 516 through 522 )
10X-RAY DIFFRACTION10chain 'B' and (resid 523 through 535 )
11X-RAY DIFFRACTION11chain 'B' and (resid 536 through 549 )
12X-RAY DIFFRACTION12chain 'C' and (resid 29 through 46 )
13X-RAY DIFFRACTION13chain 'C' and (resid 47 through 68 )
14X-RAY DIFFRACTION14chain 'C' and (resid 69 through 84 )
15X-RAY DIFFRACTION15chain 'C' and (resid 85 through 110 )
16X-RAY DIFFRACTION16chain 'D' and (resid 454 through 466 )
17X-RAY DIFFRACTION17chain 'D' and (resid 467 through 479 )
18X-RAY DIFFRACTION18chain 'D' and (resid 480 through 488 )
19X-RAY DIFFRACTION19chain 'D' and (resid 489 through 499 )
20X-RAY DIFFRACTION20chain 'D' and (resid 500 through 515 )
21X-RAY DIFFRACTION21chain 'D' and (resid 516 through 530 )
22X-RAY DIFFRACTION22chain 'D' and (resid 531 through 535 )
23X-RAY DIFFRACTION23chain 'D' and (resid 536 through 547 )

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