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- PDB-5x7z: CRYSTAL STRUCTURE OF MYCOBACTERIUM TUBERCULOSIS MARR FAMILY PROTE... -

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Basic information

Entry
Database: PDB / ID: 5x7z
TitleCRYSTAL STRUCTURE OF MYCOBACTERIUM TUBERCULOSIS MARR FAMILY PROTEIN RV2887 COMPLEX WITH P-AMINOSALICYLIC ACID
ComponentsUncharacterized HTH-type transcriptional regulator Rv2887
KeywordsTRANSCRIPTION / WHTH MOTIF / HTH-TYPE TRANSCRIPTIONAL REGULATOR / DNA BINDING / P-AMINOSALICYLIC ACID BINDING / SALICYLIC ACID BINDING
Function / homology
Function and homology information


response to stress / DNA-binding transcription factor activity / regulation of DNA-templated transcription / DNA binding
Similarity search - Function
Transcriptional regulator MarR-type, conserved site / MarR-type HTH domain signature. / : / MarR family / MarR-type HTH domain profile. / helix_turn_helix multiple antibiotic resistance protein / MarR-type HTH domain / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
2-HYDROXY-4-AMINOBENZOIC ACID / HTH-type transcriptional repressor Rv2887
Similarity search - Component
Biological speciesMycobacterium tuberculosis H37Rv (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsGao, Y.R. / Li, D.F. / Wang, D.C. / Bi, L.J.
CitationJournal: Sci Rep / Year: 2017
Title: Structural analysis of the regulatory mechanism of MarR protein Rv2887 in M. tuberculosis
Authors: Gao, Y.R. / Li, D.F. / Fleming, J. / Zhou, Y.F. / Liu, Y. / Deng, J.Y. / Zhou, L. / Zhou, J. / Zhu, G.F. / Zhang, X.E. / Wang, D.C. / Bi, L.J.
History
DepositionFeb 28, 2017Deposition site: PDBJ / Processing site: PDBJ
SupersessionAug 9, 2017ID: 5HSL
Revision 1.0Aug 9, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Mar 12, 2025Group: Database references / Structure summary / Category: pdbx_database_related / pdbx_entry_details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Uncharacterized HTH-type transcriptional regulator Rv2887
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,1662
Polymers17,0131
Non-polymers1531
Water61334
1
A: Uncharacterized HTH-type transcriptional regulator Rv2887
hetero molecules

A: Uncharacterized HTH-type transcriptional regulator Rv2887
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,3324
Polymers34,0252
Non-polymers3062
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area4650 Å2
ΔGint-27 kcal/mol
Surface area13520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.810, 86.870, 43.560
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Uncharacterized HTH-type transcriptional regulator Rv2887


Mass: 17012.662 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis H37Rv (bacteria)
Strain: H37Rv / Gene: Rv2887, MTCY274.18 / Plasmid: pET-28a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P9WME9
#2: Chemical ChemComp-BHA / 2-HYDROXY-4-AMINOBENZOIC ACID


Mass: 153.135 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H7NO3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 34 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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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: 2.41 Å3/Da / Density % sol: 49.04 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 3.5 / Details: 0.1M CITRIC ACID, PH 3.5, 2.0M AMMONIUM SULFATE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9791 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 28, 2013 / Details: MIRRORS
RadiationMonochromator: DOUBLE CRYSTAL (SI 111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.2→27.454 Å / Num. obs: 8664 / % possible obs: 99.7 % / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Biso Wilson estimate: 40.8 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.117 / Rpim(I) all: 0.05 / Rsym value: 0.117 / Net I/av σ(I): 3.6 / Net I/σ(I): 11
Reflection shellResolution: 2.2→2.32 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.821 / Mean I/σ(I) obs: 3.2 / Num. unique obs: 1245 / CC1/2: 0.91 / Rpim(I) all: 0.331 / Rsym value: 0.821 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
iMOSFLMdata reduction
SCALAdata scaling
PHASESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5HSM

5hsm


Resolution: 2.2→27.454 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 25.8
RfactorNum. reflection% reflectionSelection details
Rfree0.2483 864 9.98 %RANDOM
Rwork0.2049 ---
obs0.2095 8654 99.61 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.2→27.454 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms969 0 11 34 1014
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011992
X-RAY DIFFRACTIONf_angle_d0.9951342
X-RAY DIFFRACTIONf_dihedral_angle_d12.947627
X-RAY DIFFRACTIONf_chiral_restr0.057161
X-RAY DIFFRACTIONf_plane_restr0.007173
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2003-2.33810.26581400.20781276X-RAY DIFFRACTION100
2.3381-2.51850.27611410.21911269X-RAY DIFFRACTION100
2.5185-2.77170.27171440.21831291X-RAY DIFFRACTION100
2.7717-3.17230.28381380.23721274X-RAY DIFFRACTION99
3.1723-3.99480.27231460.19371306X-RAY DIFFRACTION100
3.9948-27.45570.21081550.19511374X-RAY DIFFRACTION100
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)
15.8292-1.655-1.9931.68154.9172-0.2332-0.2027-0.37020.57860.45660.51680.3383-0.4155-0.18680.2986-0.02680.01650.31950.05470.280224.29212.87547.3115
24.38670.62271.93637.6970.47445.7872-0.26040.174-0.2163-1.23490.45821.7392-0.1729-0.962-0.18710.46750.0194-0.14250.48680.11840.698712.878713.6628-2.461
33.2378-0.641-0.27058.58550.71630.0766-0.879-0.9058-0.87230.04570.7388-0.599-1.2045-0.55820.28721.84440.4459-0.08631.23540.14811.14544.455524.6324-15.5215
46.0474-3.13913.74696.5183-1.8684.0405-0.1856-0.07280.1386-0.04760.43460.3294-0.48080.21-0.25630.4207-0.02210.08910.35770.01530.278923.651318.6252.6406
54.14283.20564.71834.9733.52435.3988-0.22660.2197-0.1867-0.58340.3254-0.624-1.0510.5411-0.09260.29-0.04880.04360.4068-0.0330.292938.70574.6074-1.4711
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 7 through 31 )
2X-RAY DIFFRACTION2chain 'A' and (resid 32 through 80 )
3X-RAY DIFFRACTION3chain 'A' and (resid 81 through 90 )
4X-RAY DIFFRACTION4chain 'A' and (resid 91 through 120 )
5X-RAY DIFFRACTION5chain 'A' and (resid 121 through 138 )

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