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Yorodumi- PDB-2b6c: Predicted DNA alkylation repair enzyme from Enterococcus faecalis. -
+Open data
-Basic information
Entry | Database: PDB / ID: 2b6c | ||||||
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Title | Predicted DNA alkylation repair enzyme from Enterococcus faecalis. | ||||||
Components | hypothetical protein EF3068 | ||||||
Keywords | STRUCTURAL GENOMICS / UNKNOWN FUNCTION / structural genomis / DNA repair enzyme / PSI / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG | ||||||
Function / homology | Function and homology information ARM repeat fold / Hypothetical protein (EF3068) / ARM repeat domains / DNA alkylation repair enzyme / DNA alkylation repair enzyme / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Armadillo-type fold / Up-down Bundle / Mainly Alpha Similarity search - Domain/homology | ||||||
Biological species | Enterococcus faecalis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.1 Å | ||||||
Authors | Osipiuk, J. / Hatzos, C. / Moy, S. / Collart, F. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG) | ||||||
Citation | Journal: To be Published Title: Xray structure of predicted DNA alkylation repair enzyme from Enterococcus faecalis. Authors: Osipiuk, J. / Hatzos, C. / Moy, S. / Collart, F. / Joachimiak, A. | ||||||
History |
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Remark 300 | Author states that biological unit for the protein is not yet known |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2b6c.cif.gz | 108.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2b6c.ent.gz | 90.1 KB | Display | PDB format |
PDBx/mmJSON format | 2b6c.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2b6c_validation.pdf.gz | 475.6 KB | Display | wwPDB validaton report |
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Full document | 2b6c_full_validation.pdf.gz | 481.6 KB | Display | |
Data in XML | 2b6c_validation.xml.gz | 21.7 KB | Display | |
Data in CIF | 2b6c_validation.cif.gz | 31.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b6/2b6c ftp://data.pdbj.org/pub/pdb/validation_reports/b6/2b6c | 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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Details | the biological assembly is unknown |
-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 26140.168 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Enterococcus faecalis (bacteria) / Gene: EF3068 / Plasmid: pMCSG7 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q82ZI8 |
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-Non-polymers , 5 types, 317 molecules
#2: Chemical | ChemComp-SO4 / #3: Chemical | ChemComp-CL / | #4: Chemical | #5: Chemical | ChemComp-GOL / #6: 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: 3.1 Å3/Da / Density % sol: 60.4 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: 0.1 M bis-tris, 2 M ammonium sulfate , pH 5.5, 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 7, 2005 |
Radiation | Monochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→40 Å / Num. all: 36311 / Num. obs: 36311 / % possible obs: 96.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 15.8 % / Rmerge(I) obs: 0.154 / Net I/σ(I): 18 |
Reflection shell | Resolution: 2.1→2.16 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.499 / Mean I/σ(I) obs: 2.25 / Num. unique all: 2285 / % possible all: 73.8 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.1→40 Å / Cor.coef. Fo:Fc: 0.955 / SU B: 5.262 / SU ML: 0.074 / TLS residual ADP flag: LIKELY RESIDUAL / σ(F): 0 / σ(I): 0 / ESU R: 0.155 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. ALL DATA WERE USED IN FINAL ROUND OF REFINEMENT. R-FACTOR-ALL CORRESPONDS TO DEPOSITED FILE. R-WORK AND R-FREE FACTORS ARE TAKEN FROM ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. ALL DATA WERE USED IN FINAL ROUND OF REFINEMENT. R-FACTOR-ALL CORRESPONDS TO DEPOSITED FILE. R-WORK AND R-FREE FACTORS ARE TAKEN FROM SECOND TO LAST ROUND OF REFINEMENT WHICH USED TEST DATA SET.
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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: 18.558 Å2
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Refinement step | Cycle: LAST / Resolution: 2.1→40 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.101→2.156 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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