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Yorodumi- PDB-1z7u: Crystal Structure of the Putitive Transcriptional Regulator of Ma... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1z7u | ||||||
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Title | Crystal Structure of the Putitive Transcriptional Regulator of MarR Family from Enterococcus faecalis V583 | ||||||
Components | hypothetical protein EF0647 | ||||||
Keywords | STRUCTURAL GENOMICS / UNKNOWN FUNCTION / winged-helix-turn-helix / MarR / PSI / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG | ||||||
Function / homology | Function and homology information Helix-turn-helix, HxlR type / HxlR-like helix-turn-helix / HxlR-type HTH domain profile. / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / Orthogonal Bundle / Mainly Alpha Similarity search - Domain/homology | ||||||
Biological species | Enterococcus faecalis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.2 Å | ||||||
Authors | Kim, Y. / Wu, R. / Collart, F. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG) | ||||||
Citation | Journal: To be Published Title: Crystal Structure of the Putitive Transcriptional Regulator of MarR Family from Enterococcus faecalis Authors: Kim, Y. / Wu, R. / Collart, F. / Joachimiak, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1z7u.cif.gz | 59.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1z7u.ent.gz | 48.7 KB | Display | PDB format |
PDBx/mmJSON format | 1z7u.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1z7u_validation.pdf.gz | 439.2 KB | Display | wwPDB validaton report |
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Full document | 1z7u_full_validation.pdf.gz | 442.5 KB | Display | |
Data in XML | 1z7u_validation.xml.gz | 12.8 KB | Display | |
Data in CIF | 1z7u_validation.cif.gz | 18 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/z7/1z7u ftp://data.pdbj.org/pub/pdb/validation_reports/z7/1z7u | HTTPS FTP |
-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 13010.175 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Enterococcus faecalis (bacteria) / Strain: V583 / Plasmid: pMCSG7 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21DE3 / References: UniProt: Q838C3 #2: Chemical | ChemComp-FMT / | #3: 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: 3.2 Å3/Da / Density % sol: 61.5 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7 Details: BIS-TRIS-PROPANE, potassium sodium tartrate tetrahydrated, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.9792 Å |
Detector | Type: SBC-3 / Detector: CCD / Date: Mar 17, 2005 / Details: mirrors |
Radiation | Monochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→57.93 Å / Num. all: 15317 / Num. obs: 14767 / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 11.5 % / Rmerge(I) obs: 0.095 / Net I/σ(I): 7.6 |
Reflection shell | Resolution: 2.2→2.28 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.482 / Mean I/σ(I) obs: 1.8 / % possible all: 79.7 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.2→57.93 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.9 / SU B: 12.149 / SU ML: 0.164 / Cross valid method: THROUGHOUT / ESU R: 0.318 / ESU R Free: 0.242 Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES 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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 31.428 Å2
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Refinement step | Cycle: LAST / Resolution: 2.2→57.93 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.257 Å / Total num. of bins used: 20 /
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