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- PDB-3qyx: Crystal structure of Mycobacterium tuberculosis EspR in complex w... -

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Basic information

Entry
Database: PDB / ID: 3qyx
TitleCrystal structure of Mycobacterium tuberculosis EspR in complex with a small DNA fragment
Components
  • 5'-D(*A*CP*GP*CP*CP*GP*AP*AP*TP*C)-3'
  • ESX-1 secretion-associated regulator EspR
KeywordsTranscription/DNA / N-terminal HTH motif / C-terminal dimerization domain / DNA-binding / Transcription factor / Dimer of dimers binding DNA / Transcription activator / Transcription-DNA complex
Function / homology
Function and homology information


response to host immune response / nucleoid / regulation of protein secretion / peptidoglycan-based cell wall / positive regulation of DNA-templated transcription / DNA binding / extracellular region / identical protein binding / plasma membrane / cytoplasm / cytosol
Similarity search - Function
lambda repressor-like DNA-binding domains / Cro/C1-type helix-turn-helix domain / 434 Repressor (Amino-terminal Domain) / Lambda repressor-like, DNA-binding domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
DNA / Nucleoid-associated protein EspR / Nucleoid-associated protein EspR
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.75 Å
AuthorsBlasco, B. / Pojer, F. / Cole, S.T.
CitationJournal: Mol.Microbiol. / Year: 2011
Title: Atypical DNA recognition mechanism used by the EspR virulence regulator of Mycobacterium tuberculosis.
Authors: Blasco, B. / Stenta, M. / Alonso-Sarduy, L. / Dietler, G. / Peraro, M.D. / Cole, S.T. / Pojer, F.
History
DepositionMar 4, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 14, 2011Provider: repository / Type: Initial release
Revision 1.1Nov 16, 2011Group: Database references
Revision 1.2Feb 21, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.3Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ESX-1 secretion-associated regulator EspR
D: ESX-1 secretion-associated regulator EspR
B: ESX-1 secretion-associated regulator EspR
C: ESX-1 secretion-associated regulator EspR
E: 5'-D(*A*CP*GP*CP*CP*GP*AP*AP*TP*C)-3'


Theoretical massNumber of molelcules
Total (without water)61,9805
Polymers61,9805
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)86.955, 86.955, 130.363
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32

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Components

#1: Protein
ESX-1 secretion-associated regulator EspR


Mass: 14741.597 Da / Num. of mol.: 4 / Fragment: unp residues 2-132
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37Rv / Gene: espR, MT3964, Rv3849 / Plasmid: pHis9gw / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P96228, UniProt: P9WJB7*PLUS
#2: DNA chain 5'-D(*A*CP*GP*CP*CP*GP*AP*AP*TP*C)-3'


Mass: 3013.995 Da / Num. of mol.: 1 / Source method: obtained synthetically

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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: 4.63 Å3/Da / Density % sol: 73.42 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 20% PEG 3350, 0.15 M DL-malic acid, VAPOR DIFFUSION, HANGING DROP, temperature 277.15K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97298 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 11, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97298 Å / Relative weight: 1
ReflectionResolution: 3.75→75.31 Å / Num. obs: 10617 / % possible obs: 98.2 % / Redundancy: 2.6 % / Rmerge(I) obs: 0.126 / Net I/σ(I): 10
Reflection shellResolution: 3.75→3.97 Å / Redundancy: 2.5 % / Mean I/σ(I) obs: 2.7 / % possible all: 96.8

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Processing

Software
NameVersionClassification
XDSdata scaling
CCP4model building
PHENIXmodel building
PHENIX(phenix.refine: 1.7_650)refinement
XDSdata reduction
CCP4phasing
PHENIXphasing
REFMAC5.5.0109refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: WT EspR

Resolution: 3.75→43.59 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.894 / SU B: 0.015 / SU ML: 0 / Cross valid method: THROUGHOUT / ESU R: 0.489 / ESU R Free: 0.556 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23456 533 4.8 %RANDOM
Rwork0.20612 ---
obs0.20743 10617 98.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 81.634 Å2
Baniso -1Baniso -2Baniso -3
1-2.06 Å21.03 Å20 Å2
2--2.06 Å20 Å2
3----3.1 Å2
Refinement stepCycle: LAST / Resolution: 3.75→43.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4074 98 0 0 4172
LS refinement shellResolution: 3.754→3.851 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.256 39 -
Rwork0.286 726 -
obs--94.21 %

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