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- PDB-6jmi: Crystal structure of M.tuberculosis Rv0081 -

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Basic information

Entry
Database: PDB / ID: 6jmi
TitleCrystal structure of M.tuberculosis Rv0081
ComponentsUncharacterized HTH-type transcriptional regulator Rv0081
KeywordsTRANSCRIPTION / hypoxia / ArsR/SmtB / FHL regulator / regulatory hub
Function / homology
Function and homology information


DNA-binding transcription factor activity / DNA binding / plasma membrane
Similarity search - Function
Helix-turn-helix domain / ArsR-type HTH domain profile. / helix_turn_helix, Arsenical Resistance Operon Repressor / HTH ArsR-type DNA-binding domain / ArsR-like helix-turn-helix domain / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
Uncharacterized HTH-type transcriptional regulator Rv0081
Similarity search - Component
Biological speciesMycobacterium tuberculosis H37Rv (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.896 Å
AuthorsKumar, A. / Phulera, S. / Mande, C.S.
Funding support India, 2items
OrganizationGrant numberCountry
Department of Biotechnology (India)BT/PR3260/BRB/10/967/2011 India
Department of Biotechnology (India)BT/PR15450/COE/34/46/2016 India
CitationJournal: Febs Lett. / Year: 2019
Title: Structural basis of hypoxic gene regulation by the Rv0081 transcription factor of Mycobacterium tuberculosis.
Authors: Kumar, A. / Phulera, S. / Rizvi, A. / Sonawane, P.J. / Panwar, H.S. / Banerjee, S. / Sahu, A. / Mande, S.C.
History
DepositionMar 11, 2019Deposition site: PDBJ / Processing site: PDBJ
SupersessionApr 10, 2019ID: 5XPQ
Revision 1.0Apr 10, 2019Provider: repository / Type: Initial release
Revision 1.1Apr 17, 2019Group: Author supporting evidence / Data collection / Database references
Category: citation / citation_author / pdbx_audit_support
Item: _citation.journal_abbrev / _citation.journal_id_ISSN ..._citation.journal_abbrev / _citation.journal_id_ISSN / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name / _pdbx_audit_support.grant_number
Revision 1.2May 22, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_abbrev / _citation.journal_id_ISSN ..._citation.journal_abbrev / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Uncharacterized HTH-type transcriptional regulator Rv0081
B: Uncharacterized HTH-type transcriptional regulator Rv0081
C: Uncharacterized HTH-type transcriptional regulator Rv0081
D: Uncharacterized HTH-type transcriptional regulator Rv0081
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,7498
Polymers49,3654
Non-polymers3844
Water0
1
A: Uncharacterized HTH-type transcriptional regulator Rv0081
D: Uncharacterized HTH-type transcriptional regulator Rv0081
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,8754
Polymers24,6822
Non-polymers1922
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3440 Å2
ΔGint-54 kcal/mol
Surface area9500 Å2
MethodPISA
2
B: Uncharacterized HTH-type transcriptional regulator Rv0081
C: Uncharacterized HTH-type transcriptional regulator Rv0081
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,8754
Polymers24,6822
Non-polymers1922
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3480 Å2
ΔGint-50 kcal/mol
Surface area10100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.317, 63.317, 262.604
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein
Uncharacterized HTH-type transcriptional regulator Rv0081


Mass: 12341.243 Da / Num. of mol.: 4 / Fragment: UNP residues 2-114
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis H37Rv (bacteria)
Strain: H37Rv / Gene: Rv0081 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P9WMI7
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION

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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: 2.76 Å3/Da / Density % sol: 53.86 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 0.1M CH3COONa , (0.2-0.4) M NH4(SO4)2, 25% w/VPEG 4000
PH range: 4.8

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 0.9686 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Dec 16, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9686 Å / Relative weight: 1
ReflectionResolution: 2.896→45.58 Å / Num. obs: 12678 / % possible obs: 99.54 % / Redundancy: 13.3 % / Biso Wilson estimate: 78.52 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.192 / Rpim(I) all: 0.054 / Rrim(I) all: 0.201 / Χ2: 0.97 / Net I/av σ(I): 1.3 / Net I/σ(I): 11.6
Reflection shellResolution: 2.9→3.07 Å / Redundancy: 13.3 % / Rmerge(I) obs: 2.141 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 1941 / CC1/2: 0.585 / Rpim(I) all: 0.814 / Rrim(I) all: 2.226 / Χ2: 0.78 / % possible all: 98.5

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
XDSdata procesiingdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.896→45.575 Å / SU ML: 0.46 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 32.3
RfactorNum. reflection% reflectionSelection details
Rfree0.3013 1264 9.98 %0.1
Rwork0.261 ---
obs0.265 12660 99.53 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.896→45.575 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2768 0 20 0 2788
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0022806
X-RAY DIFFRACTIONf_angle_d0.4693802
X-RAY DIFFRACTIONf_dihedral_angle_d6.6971722
X-RAY DIFFRACTIONf_chiral_restr0.034481
X-RAY DIFFRACTIONf_plane_restr0.003477
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8956-3.01150.39011340.35321189X-RAY DIFFRACTION97
3.0115-3.14860.43221380.34221221X-RAY DIFFRACTION100
3.1486-3.31450.31141320.34921253X-RAY DIFFRACTION100
3.3145-3.52210.34111390.30171246X-RAY DIFFRACTION100
3.5221-3.79390.32821360.27581235X-RAY DIFFRACTION100
3.7939-4.17550.32471400.24991265X-RAY DIFFRACTION100
4.1755-4.77920.23081430.2231279X-RAY DIFFRACTION100
4.7792-6.01910.31511440.24971300X-RAY DIFFRACTION100
6.0191-45.58030.26861580.23561408X-RAY DIFFRACTION99
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)
11.9505-0.5298-0.37793.28-0.61145.6726-0.1662-0.0595-0.38470.06760.13970.20120.16660.2045-0.06350.35470.0150.01770.5964-0.00380.5566155.314452.5655351.0791
22.62740.11922.02191.9594-0.62522.83540.1492-0.60110.02720.379-0.270.3516-0.0497-0.33930.11430.3960.00550.08950.6417-0.18150.5216144.028358.4122388.6136
33.426-0.95750.4761.5217-0.41093.74150.22490.0905-0.46560.3474-0.0076-0.15610.24610.4589-0.13990.41790.1259-0.00140.6941-0.07080.534163.566254.7935383.2795
43.25151.5593-2.52982.8649-0.36584.9389-0.00810.05050.696-0.2067-0.08780.4211-1.0457-0.52290.11090.7640.3197-0.20510.6838-0.11270.5967146.086267.8988354.8144
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 3:102 )A3 - 102
2X-RAY DIFFRACTION2( CHAIN B AND RESID 4:102 )B4 - 102
3X-RAY DIFFRACTION3( CHAIN C AND RESID 4:102 )C4 - 102
4X-RAY DIFFRACTION4( CHAIN D AND RESID 4:101 )D4 - 101

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