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Yorodumi- PDB-2fml: Crystal structure of MutT/nudix family protein from Enterococcus ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2fml | ||||||
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Title | Crystal structure of MutT/nudix family protein from Enterococcus faecalis | ||||||
Components | MutT/nudix family protein | ||||||
Keywords | STRUCTURAL GENOMICS / UNKNOWN FUNCTION / MutT/nudix family protein / Enterococcus faecalis / 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: 2.26 Å | ||||||
Authors | Chang, C. / Quartey, P. / Moy, S. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG) | ||||||
Citation | Journal: To be Published Title: Crystal structure of MutT/nudix family protein from Enterococcus faecalis Authors: Chang, C. / Quartey, P. / 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 | 2fml.cif.gz | 118 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2fml.ent.gz | 98.3 KB | Display | PDB format |
PDBx/mmJSON format | 2fml.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fm/2fml ftp://data.pdbj.org/pub/pdb/validation_reports/fm/2fml | 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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Unit cell |
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-Components
#1: Protein | Mass: 31694.084 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Enterococcus faecalis (bacteria) / Plasmid: pMCSG / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) Derivatives / References: GenBank: 29344646, UniProt: Q830S2*PLUS #2: Chemical | ChemComp-GOL / | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.88 Å3/Da / Density % sol: 57.28 % |
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: MgCl2, HEPES, PEG550, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 290K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97929 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 31, 2005 |
Radiation | Monochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97929 Å / Relative weight: 1 |
Reflection | Resolution: 2.26→50 Å / Num. all: 35087 / Num. obs: 34806 / % possible obs: 99.2 % / Observed criterion σ(I): -3 / Redundancy: 7 % / Rmerge(I) obs: 0.062 / Net I/σ(I): 45.3 |
Reflection shell | Resolution: 2.26→2.34 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.289 / Mean I/σ(I) obs: 5.89 / % possible all: 96.6 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.26→50 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.929 / SU B: 11.087 / SU ML: 0.146 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.24 / ESU R Free: 0.204 / Stereochemistry target values: MAXIMUM LIKELIHOOD / 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: 54.275 Å2
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Refinement step | Cycle: LAST / Resolution: 2.26→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.26→2.319 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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