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Yorodumi- PDB-3cex: Crystal structure of the conserved protein of locus EF_3021 from ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3cex | ||||||
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Title | Crystal structure of the conserved protein of locus EF_3021 from Enterococcus faecalis | ||||||
Components | Uncharacterized protein | ||||||
Keywords | STRUCTURAL GENOMICS / UNKNOWN FUNCTION / Enterococcus faecalis / EF_3021 / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG | ||||||
Function / homology | Function and homology information Protein of unknown function (DUF664) / DinB-like domain / DinB superfamily / dinb family like domain / DinB/YfiT-like putative metalloenzymes / Four Helix Bundle (Hemerythrin (Met), subunit A) / Up-down Bundle / Mainly Alpha Similarity search - Domain/homology | ||||||
Biological species | Enterococcus faecalis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / MAD / Resolution: 2 Å | ||||||
Authors | Cuff, M.E. / Wu, R. / Moy, S. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG) | ||||||
Citation | Journal: TO BE PUBLISHED Title: Structure of the conserved protein of locus EF_3021 from Enterococcus faecalis. Authors: Cuff, M.E. / Wu, R. / 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 | 3cex.cif.gz | 82.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3cex.ent.gz | 65.8 KB | Display | PDB format |
PDBx/mmJSON format | 3cex.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3cex_validation.pdf.gz | 452.3 KB | Display | wwPDB validaton report |
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Full document | 3cex_full_validation.pdf.gz | 453.8 KB | Display | |
Data in XML | 3cex_validation.xml.gz | 16.2 KB | Display | |
Data in CIF | 3cex_validation.cif.gz | 23 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ce/3cex ftp://data.pdbj.org/pub/pdb/validation_reports/ce/3cex | HTTPS FTP |
-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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Details | AUTHORS STATE THAT THE BIOLOGICAL UNIT IS UNKNOWN |
-Components
#1: Protein | Mass: 19788.535 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Enterococcus faecalis (bacteria) / Strain: V583 / Gene: EF_3021 / Plasmid: pMCSG7 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q82ZN0 #2: Chemical | #3: Chemical | #4: 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: 2.28 Å3/Da / Density % sol: 46.05 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 1M Trisodium citrate, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9793 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 3, 2007 |
Radiation | Monochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 |
Reflection | Resolution: 2→35.9 Å / Num. all: 23947 / Num. obs: 23947 / % possible obs: 98.91 % / Observed criterion σ(I): -3 / Redundancy: 6.9 % / Biso Wilson estimate: 23.4 Å2 / Rmerge(I) obs: 0.107 / Net I/σ(I): 6.6 |
Reflection shell | Resolution: 2→2.05 Å / Redundancy: 5 % / Rmerge(I) obs: 0.41 / Mean I/σ(I) obs: 2.4 / Num. unique all: 1506 / % possible all: 89.32 |
-Phasing
Phasing | Method: MAD | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Phasing MAD | D res high: 2.01 Å / D res low: 50 Å / FOM : 0.168 / FOM acentric: 0.177 / FOM centric: 0 / Reflection: 23729 / Reflection acentric: 22468 / Reflection centric: 1261 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Phasing MAD set | R cullis acentric: 1.62 / R cullis centric: 1 / Highest resolution: 2.01 Å / Lowest resolution: 50 Å / Loc acentric: 0.1 / Loc centric: 0.1 / Power acentric: 0 / Power centric: 0 / Reflection acentric: 22468 / Reflection centric: 1261 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Phasing MAD set shell | ID: 1 / R cullis centric: 1 / Power acentric: 0 / Power centric: 0
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Phasing MAD set site |
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Phasing MAD shell |
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Phasing dm | Method: Solvent flattening and Histogram matching / Reflection: 23729 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Phasing dm shell |
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-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2→35.9 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.952 / SU B: 7.472 / SU ML: 0.105 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.173 / ESU R Free: 0.151 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: 27.35 Å2
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Refinement step | Cycle: LAST / Resolution: 2→35.9 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.05 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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