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Yorodumi- PDB-4xrf: Crystal structure of MepR like protein complexed with pseudoligands -
+Open data
-Basic information
Entry | Database: PDB / ID: 4xrf | ||||||
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Title | Crystal structure of MepR like protein complexed with pseudoligands | ||||||
Components | Transcriptional regulator, MarR familyTranscriptional regulation | ||||||
Keywords | TRANSCRIPTION / WINGED HELIX TURN HELIX TRANSCRIPTION FACTOR | ||||||
Function / homology | Function and homology information transcription cis-regulatory region binding / DNA-binding transcription factor activity / regulation of DNA-templated transcription Similarity search - Function | ||||||
Biological species | Bacillus cereus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.16 Å | ||||||
Authors | Hong, M. / Kim, M.I. / Cho, M.U. | ||||||
Citation | Journal: to be published Title: Crystal structure of MepR like protein complexed with pseudoligands Authors: Hong, M. / Kim, M.I. / Cho, M.U. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4xrf.cif.gz | 77.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4xrf.ent.gz | 57.7 KB | Display | PDB format |
PDBx/mmJSON format | 4xrf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xr/4xrf ftp://data.pdbj.org/pub/pdb/validation_reports/xr/4xrf | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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Details | The biological assembly is a hexamer generated from the dimer in the asymmetric unit by the operations: -X+Y, Y, -Z |
-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 16531.305 Da / Num. of mol.: 1 / Fragment: UNP residues 5-146 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus cereus (strain ATCC 14579 / DSM 31) (bacteria) Strain: ATCC 14579 / DSM 31 / Gene: BC_0657 / Plasmid: pET49b / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q81HX3 |
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-Non-polymers , 7 types, 76 molecules
#2: Chemical | ChemComp-PO4 / #3: Chemical | ChemComp-ISQ / | #4: Chemical | ChemComp-DAO / | #5: Chemical | #6: Chemical | ChemComp-NI / | #7: Chemical | ChemComp-SO4 / | #8: Water | ChemComp-HOH / | |
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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: 3.63 Å3/Da / Density % sol: 66.16 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4 / Details: 0.1M phosphate citrate, 2.4 M ammonium sulfate |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.97958 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Apr 8, 2014 / Details: certical focusing toroidal, rhodium coated | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: DCM Si crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97958 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.16→50 Å / Num. obs: 13502 / % possible obs: 99.1 % / Redundancy: 20.6 % / Rmerge(I) obs: 0.094 / Χ2: 5.479 / Net I/av σ(I): 83.969 / Net I/σ(I): 16.8 / Num. measured all: 277710 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: 0
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.16→26.72 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.932 / SU B: 9.708 / SU ML: 0.133 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.193 / ESU R Free: 0.167 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : WITH TLS ADDED
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 97.63 Å2 / Biso mean: 45.695 Å2 / Biso min: 20.67 Å2
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Refinement step | Cycle: final / Resolution: 2.16→26.72 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.162→2.219 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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