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Yorodumi- PDB-3qyx: Crystal structure of Mycobacterium tuberculosis EspR in complex w... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3qyx | ||||||
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Title | Crystal structure of Mycobacterium tuberculosis EspR in complex with a small DNA fragment | ||||||
Components |
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Keywords | Transcription/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 / regulation of DNA-templated transcription / DNA binding / extracellular region / identical protein binding / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Mycobacterium tuberculosis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.75 Å | ||||||
Authors | Blasco, B. / Pojer, F. / Cole, S.T. | ||||||
Citation | Journal: 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3qyx.cif.gz | 113.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3qyx.ent.gz | 88.6 KB | Display | PDB format |
PDBx/mmJSON format | 3qyx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qy/3qyx ftp://data.pdbj.org/pub/pdb/validation_reports/qy/3qyx | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | 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 | | Mass: 3013.995 Da / Num. of mol.: 1 / Source method: obtained synthetically |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 4.63 Å3/Da / Density % sol: 73.42 % |
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Crystal grow | Temperature: 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 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97298 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 11, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97298 Å / Relative weight: 1 |
Reflection | Resolution: 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 shell | Resolution: 3.75→3.97 Å / Redundancy: 2.5 % / Mean I/σ(I) obs: 2.7 / % possible all: 96.8 |
-Processing
Software |
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Refinement | Method 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
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||
Displacement parameters | Biso mean: 81.634 Å2
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Refinement step | Cycle: LAST / Resolution: 3.75→43.59 Å
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LS refinement shell | Resolution: 3.754→3.851 Å / Total num. of bins used: 20
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