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- PDB-7kuf: Transcription activation subcomplex with WhiB7 bound to SigmaAr4-... -

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Basic information

Entry
Database: PDB / ID: 7kuf
TitleTranscription activation subcomplex with WhiB7 bound to SigmaAr4-RNAP Beta flap tip chimera and DNA
Components
  • DNA (5'-D(*CP*AP*GP*AP*AP*AP*AP*TP*CP*GP*GP*TP*TP*GP*TP*GP*GP*T)-3')
  • DNA (5'-D(*GP*AP*CP*CP*AP*CP*AP*AP*CP*CP*GP*AP*TP*TP*TP*TP*CP*T)-3')
  • Probable transcriptional regulator WhiB7
  • RNA polymerase sigma factor, DNA-directed RNA polymerase subunit beta chimera
KeywordsTRANSCRIPTION / Redox-sensitive / Iron-sulfur cluster / activator
Function / homology
Function and homology information


dinitrosyl-iron complex binding / protein-disulfide reductase [NAD(P)H] activity / response to fatty acid / sigma factor activity / DNA-directed RNA polymerase complex / cell redox homeostasis / DNA-templated transcription initiation / ribonucleoside binding / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase ...dinitrosyl-iron complex binding / protein-disulfide reductase [NAD(P)H] activity / response to fatty acid / sigma factor activity / DNA-directed RNA polymerase complex / cell redox homeostasis / 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 / negative regulation of DNA-templated transcription / DNA-templated transcription / DNA binding / metal ion binding / cytoplasm
Similarity search - Function
AT hook motif / Transcription factor WhiB / WhiB-like iron-sulfur binding domain / Transcription factor WhiB / 4Fe-4S WhiB-like (Wbl)-type iron-sulfur binding domain profile. / AT hook, DNA-binding motif / Sigma-70 factors family signature 1. / RNA polymerase sigma factor RpoD, C-terminal / RNA polymerase sigma factor RpoD / : ...AT hook motif / Transcription factor WhiB / WhiB-like iron-sulfur binding domain / Transcription factor WhiB / 4Fe-4S WhiB-like (Wbl)-type iron-sulfur binding domain profile. / AT hook, DNA-binding motif / 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 / DNA / DNA (> 10) / RNA polymerase sigma factor SigA / DNA-directed RNA polymerase subunit beta / Probable transcriptional regulator WhiB7
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsWan, T. / Horova, M. / Beltran, D.G. / Li, S.R. / Zhang, L.M.
Funding support United States, 4items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)2562300224001 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35 GM138157-01 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P20 GM113126 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P30 GM103335 United States
CitationJournal: Mol.Cell / Year: 2021
Title: Structural insights into the functional divergence of WhiB-like proteins in Mycobacterium tuberculosis.
Authors: Wan, T. / Horova, M. / Beltran, D.G. / Li, S. / Wong, H.X. / Zhang, L.M.
History
DepositionNov 24, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 30, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 6, 2021Group: Database references / Category: citation / citation_author / database_2
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Oct 18, 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

Downloads & links

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Assembly

Deposited unit
A: Probable transcriptional regulator WhiB7
B: RNA polymerase sigma factor, DNA-directed RNA polymerase subunit beta chimera
C: DNA (5'-D(*CP*AP*GP*AP*AP*AP*AP*TP*CP*GP*GP*TP*TP*GP*TP*GP*GP*T)-3')
D: DNA (5'-D(*GP*AP*CP*CP*AP*CP*AP*AP*CP*CP*GP*AP*TP*TP*TP*TP*CP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,1875
Polymers33,8354
Non-polymers3521
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5640 Å2
ΔGint-46 kcal/mol
Surface area13890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.254, 69.254, 167.374
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Space group name HallP322"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+2/3
#3: -x+y,-x,z+1/3
#4: x-y,-y,-z+1/3
#5: -x,-x+y,-z+2/3
#6: y,x,-z

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Components

#1: Protein Probable transcriptional regulator WhiB7


Mass: 10153.804 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: whiB7, Rv3197A, Rv3197.1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(Gold) / References: UniProt: Q6MX01
#2: Protein RNA polymerase sigma factor, DNA-directed RNA polymerase subunit beta chimera / RNAP subunit beta / RNA polymerase subunit beta / Transcriptase subunit beta


Mass: 12650.234 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria)
Gene: sigA, ERS007670_01286, ERS007681_03833, ERS007688_01862
Production host: Escherichia coli (E. coli) / Strain (production host): BL21(Gold)
References: UniProt: A0A654TMB9, UniProt: A1KGE7, DNA-directed RNA polymerase
#3: DNA chain DNA (5'-D(*CP*AP*GP*AP*AP*AP*AP*TP*CP*GP*GP*TP*TP*GP*TP*GP*GP*T)-3')


Mass: 5595.640 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Mycobacterium tuberculosis (bacteria)
#4: DNA chain DNA (5'-D(*GP*AP*CP*CP*AP*CP*AP*AP*CP*CP*GP*AP*TP*TP*TP*TP*CP*T)-3')


Mass: 5435.542 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Mycobacterium tuberculosis (bacteria)
#5: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe4S4 / Feature type: SUBJECT OF INVESTIGATION
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: 3.42 Å3/Da / Density % sol: 69.4 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 0.2-0.3 M NH4H2PO4

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 21, 2020
Details: Flat Si Rh coated M0, Kirkpatrick-Baez flat bent Si M1 & M2
RadiationMonochromator: Liquid nitrogen-cooled double crystal Si(111)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 14675 / % possible obs: 98.1 % / Redundancy: 26.4 % / Biso Wilson estimate: 85.06 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.101 / Net I/σ(I): 33.1
Reflection shellResolution: 2.6→2.64 Å / Num. unique obs: 612 / CC1/2: 0.885 / % possible all: 83.3

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Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7KUG

7kug


Resolution: 2.6→29.99 Å / SU ML: 0.4648 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 42.2883
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2547 690 4.82 %
Rwork0.2212 13615 -
obs0.2227 14305 95.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 121.66 Å2
Refinement stepCycle: LAST / Resolution: 2.6→29.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1247 732 8 0 1987
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00722101
X-RAY DIFFRACTIONf_angle_d0.94542998
X-RAY DIFFRACTIONf_chiral_restr0.053335
X-RAY DIFFRACTIONf_plane_restr0.0062261
X-RAY DIFFRACTIONf_dihedral_angle_d31.7212845
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.80.50651130.48392494X-RAY DIFFRACTION89.43
2.8-3.090.39181580.36742723X-RAY DIFFRACTION98.63
3.09-3.530.31821400.26862613X-RAY DIFFRACTION93.1
3.53-4.450.26121090.22412836X-RAY DIFFRACTION98.76
4.45-29.990.2091700.17752949X-RAY DIFFRACTION99.33
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)
18.228795715491.22985970904-3.054235980133.507607984013.940806332776.927783459021.51026115376-1.840310853190.4493468442610.605460579157-0.885387770880.490955343765-0.552605996495-0.182637277635-0.732469860081.3876255618-0.209328723959-0.08780549746951.30843339807-0.06493241043120.99663174012114.8726069658-2.90624395627-16.2682215627
29.794488391683.95417449581-0.4368349286069.98519437951-0.1798042643882.12879051153-0.4449428177690.830877875150.8989399597110.412661045975-0.0008947011372651.244774728981.03837382375-1.4273718387-0.02555013548140.852050322305-0.0665323957904-0.01830072571361.4762970046-0.01022059047910.8279503693387.10496899047-13.0374219188-16.9574955652
32.505058799320.26110521796-2.427618971554.77849635763-1.405009437152.583927953051.073954986072.12448797381-1.22459577968-0.0398880099927-0.354931986901-0.4923276570130.5971625344891.12451708422-0.5108979525040.905224307986-0.045945800280.003803984703541.44014703226-0.002799425442950.71848953050613.7485988779-13.4758758703-23.437888185
45.987972658462.45016667241-1.046442868245.16262309348-0.2059760133648.50890640432-0.498001087302-1.578084792790.0009976492560360.20871489-0.218758531823-0.8999182262990.667041574862.063513342930.624720691010.7893245583390.130011452561-0.1051729684511.754118465870.04784500932060.8333211456219.3841137965-16.3599906499-13.0279607118
53.129841094925.076522148570.6131659651158.472972094451.342674127814.1288361167-0.8308779772010.791406672895-1.95050206318-2.755392962090.181040817444-0.3460698242031.541200690421.808883478770.7482249879141.720233773930.4327482799540.1014607887441.63095057418-0.03047771566480.87426058263212.4048527845-25.7095271185-18.5737459188
66.30368376981-1.194211853112.603585477382.097502248382.608194331366.06400542580.7098958772660.354731569226-0.1805648097150.4600385564180.180036970083-1.251565766640.986987105263-0.599977888724-0.7088185623121.731831202930.0848461400841-0.03511208589571.136281706080.06968740248910.8382109923772.0003757755-32.3052875587-26.9449153682
73.381015770712.84297538299-0.7565163309373.47519747220.9529815083282.58502936494-0.764238388822-0.03064780038041.556911482230.5978643333331.468453581951.04037518887-1.13597863984-0.504242490689-0.7962194698921.53239649094-0.0718860915159-0.03143020101891.42227332067-0.04021174741521.131154102496.534903788230.0455056078145-1.2083176953
88.495497077961.73217078839-2.997048788377.74307415802-0.8274455376876.420825377040.548217228068-1.257488149060.3195491348771.439467275280.0424247901797-0.0839021924240.7204196805810.24511633517-0.483118743631.036666032460.0846171612664-0.1149645496021.13818903443-0.07042024431290.465496796079-0.85500477515-13.53438392544.4451206429
98.540567148223.01966071868-4.072027517676.50674008608-0.8221958263537.197123056940.367597412017-1.52405508265-0.8427726203311.13382209556-0.297780032261-0.7345034309740.9988483508321.611500659680.1166515632521.061063358070.102186915925-0.08569389296711.28271615489-0.0789590521180.5671526061125.45752127055-19.0296325178-2.31185213449
100.271359093409-0.49513466157-0.2575622539341.747660962452.473079031515.598385840961.59547221302-2.079593982651.814917146190.7559007578910.850805501363-1.25026858829-2.424695398351.43210333871-0.910611221141.32737124645-0.4044336102460.09193082228142.00202226337-0.5302412046130.93282325083115.1039948822-4.77464897725-4.61316889073
111.896719846130.790657045805-2.195322359926.16961124526-0.9592065073347.40081943636-0.241126548144-2.42022678134-0.2097938317041.90047294886-0.02415194960240.2438431210320.04177812290031.40305632294-0.5359686010551.29394828375-0.287665069363-0.1284883054132.33845685302-0.3755018743280.97237107278914.8191312535-8.867240586845.28885119137
123.23741916880.9780824656353.327750280315.233334996512.632205025039.698160647781.0521825147-0.87229650508-0.7783682799381.01836708382-0.7389545510230.2301267974230.437635704185-2.72376071388-0.2118614699542.64263878969-0.224321552518-0.3353068946461.80543642692-0.3143367393910.934888733787-10.8434377453-39.7360304133-29.247691655
135.493897048992.11164252851.690156542575.422305130866.672156078268.895141239271.30064297151-0.0409912065647-0.443278909039-0.037172529202-0.581385144056-0.7111121129860.786525330866-0.406604914202-0.7169855196472.135548619640.0759077161247-0.2770192723341.3647573959-0.1470113467390.762319138392-0.564541519905-30.7709784089-16.8745244456
147.818292570290.7288811436473.725746202144.00810237992.033991386547.640168641770.960012007129-1.78028195631-1.798013036120.2898453023850.518118258677-0.1915889349693.733208840960.845230520074-1.472423555282.498832005940.257624485203-0.2982426503421.659509723060.165057780810.8790768142232.1328143392-33.45084380864.54987527517
153.648041621890.8665504672870.7185551548735.545820534691.10239335824.776448998190.31613991224-1.02824847698-0.640109978213-0.2213125268021.284699031721.484704020991.47390447886-0.224394327221-0.3076161804421.971618139740.496541075755-0.335957680531.843617363660.2803698259480.8406260696663.61940148401-27.379787759512.7197684093
165.58154639728-1.42234322293-3.30046764152.82493821397-0.3739194625572.646860500810.0769853280652-0.0366727662697-0.7680008258540.06221140517290.355290593067-0.05066916914552.13479293817-0.84466445932-0.3992636973341.98785205711-0.0692068793971-0.1721024729631.03448180596-0.07335406946130.78039773038-2.57731206686-33.6682916688-15.8317086029
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 16 through 24 )A16 - 24
2X-RAY DIFFRACTION2chain 'A' and (resid 25 through 32 )A25 - 32
3X-RAY DIFFRACTION3chain 'A' and (resid 33 through 45 )A33 - 45
4X-RAY DIFFRACTION4chain 'A' and (resid 46 through 72 )A46 - 72
5X-RAY DIFFRACTION5chain 'A' and (resid 73 through 82 )A73 - 82
6X-RAY DIFFRACTION6chain 'A' and (resid 83 through 88 )A83 - 88
7X-RAY DIFFRACTION7chain 'B' and (resid 455 through 466 )B455 - 466
8X-RAY DIFFRACTION8chain 'B' and (resid 467 through 499 )B467 - 499
9X-RAY DIFFRACTION9chain 'B' and (resid 500 through 515 )B500 - 515
10X-RAY DIFFRACTION10chain 'B' and (resid 516 through 535 )B516 - 535
11X-RAY DIFFRACTION11chain 'B' and (resid 536 through 547 )B536 - 547
12X-RAY DIFFRACTION12chain 'C' and (resid 1 through 5 )C1 - 5
13X-RAY DIFFRACTION13chain 'C' and (resid 6 through 10 )C6 - 10
14X-RAY DIFFRACTION14chain 'C' and (resid 11 through 18 )C11 - 18
15X-RAY DIFFRACTION15chain 'D' and (resid 1 through 5 )D1 - 5
16X-RAY DIFFRACTION16chain 'D' and (resid 6 through 18 )D6 - 18

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