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Yorodumi- PDB-2fhp: Crystal Structure of Putative Methylase from Enterococcus faecalis -
+Open data
-Basic information
Entry | Database: PDB / ID: 2fhp | ||||||
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Title | Crystal Structure of Putative Methylase from Enterococcus faecalis | ||||||
Components | methylase, putativeMethyltransferase | ||||||
Keywords | STRUCTURAL GENOMICS / UNKNOWN FUNCTION / alpha-beta-alpha sandwich / PSI / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Enterococcus faecalis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.6 Å | ||||||
Authors | Kim, Y. / Zhou, M. / Moy, S. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG) | ||||||
Citation | Journal: To be Published Title: Crystal Structure of Putative Methylase from Enterococcus faecalis Authors: Kim, Y. / Zhou, M. / Moy, S. / Joachimiak, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2fhp.cif.gz | 91.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2fhp.ent.gz | 74.9 KB | Display | PDB format |
PDBx/mmJSON format | 2fhp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fh/2fhp ftp://data.pdbj.org/pub/pdb/validation_reports/fh/2fhp | HTTPS FTP |
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-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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 21342.588 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: GenBank: 29344411, UniProt: Q831P8*PLUS #2: 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: 2.15 Å3/Da / Density % sol: 42.85 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 100mM HEPES pH 7.5, 25% PEG4000, VAPOR DIFFUSION, SITTING DROP, temperature 289K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9794 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 8, 2005 / Details: mirrors |
Radiation | Monochromator: double crystal monochromator, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9794 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→28.84 Å / Num. all: 46688 / Num. obs: 46453 / % possible obs: 96.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.6 % / Rmerge(I) obs: 0.091 / Net I/σ(I): 15.5 |
Reflection shell | Resolution: 1.6→1.66 Å / Redundancy: 5 % / Rmerge(I) obs: 0.184 / Mean I/σ(I) obs: 10.8 / Num. unique all: 3677 / % possible all: 76.3 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.6→28.84 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.927 / SU B: 1.523 / SU ML: 0.056 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.105 / ESU R Free: 0.103 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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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: 14.346 Å2
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Refinement step | Cycle: LAST / Resolution: 1.6→28.84 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.596→1.638 Å / Total num. of bins used: 20
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