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Yorodumi- PDB-2w4e: Structure of an N-terminally truncated Nudix hydrolase DR2204 fro... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2w4e | ||||||
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Title | Structure of an N-terminally truncated Nudix hydrolase DR2204 from Deinococcus radiodurans | ||||||
Components | MUTT/NUDIX FAMILY PROTEIN | ||||||
Keywords | HYDROLASE / ADP-RIBOSE PYROPHOSPHATASE | ||||||
Function / homology | Function and homology information nucleoside phosphate metabolic process / ribose phosphate metabolic process / hydrolase activity / cytosol Similarity search - Function | ||||||
Biological species | DEINOCOCCUS RADIODURANS (radioresistant) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å | ||||||
Authors | Goncalves, A.M.D. / Fioravanti, E. / Stelter, M. / McSweeney, S. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.F / Year: 2009 Title: Structure of an N-Terminally Truncated Nudix Hydrolase Dr2204 from Deinococcus Radiodurans. Authors: Goncalves, A.M.D. / Fioravanti, E. / Stelter, M. / Mcsweeney, S. | ||||||
History |
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Remark 700 | SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2w4e.cif.gz | 64.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2w4e.ent.gz | 48.3 KB | Display | PDB format |
PDBx/mmJSON format | 2w4e.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2w4e_validation.pdf.gz | 428.7 KB | Display | wwPDB validaton report |
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Full document | 2w4e_full_validation.pdf.gz | 430.6 KB | Display | |
Data in XML | 2w4e_validation.xml.gz | 12.9 KB | Display | |
Data in CIF | 2w4e_validation.cif.gz | 17.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/w4/2w4e ftp://data.pdbj.org/pub/pdb/validation_reports/w4/2w4e | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 15606.864 Da / Num. of mol.: 2 / Fragment: RESIDUES 56-200 Source method: isolated from a genetically manipulated source Source: (gene. exp.) DEINOCOCCUS RADIODURANS (radioresistant) Strain: R1 / Plasmid: PET151-D/TOPO / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9RSC1, ADP-ribose diphosphatase #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: 2.59 Å3/Da / Density % sol: 52 % / Description: NONE |
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Crystal grow | pH: 7 / Details: 0.2 M LINO3 20% W/V POLYETHYLENE GLYCOL 3350, pH 7 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.98 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Sep 18, 2008 / Details: TOROIDAL MIRROR |
Radiation | Monochromator: DOUBLE CRYSTAL, SI(111) OR SI(311) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 2→50 Å / Num. obs: 22215 / % possible obs: 99.7 % / Observed criterion σ(I): 2 / Redundancy: 4.4 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 11 |
Reflection shell | Resolution: 2→2.11 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.39 / Mean I/σ(I) obs: 3.6 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: SAD Starting model: NONE Resolution: 2→57.45 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.918 / SU B: 3.907 / SU ML: 0.112 / Cross valid method: THROUGHOUT / ESU R: 0.179 / ESU R Free: 0.162 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY. THE SIDE CHAIN ATOMS WITHOUT VISIBLE ELECTRON DENSITY AT 1 SIGMA WERE REMOVED FROM THE MODEL. THE FINAL ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY. THE SIDE CHAIN ATOMS WITHOUT VISIBLE ELECTRON DENSITY AT 1 SIGMA WERE REMOVED FROM THE MODEL. THE FINAL MODEL CONSISTS OF AN N-TERMINALLY TRUNCATED FORM OF THE PROTEIN MISSING THE FIRST 55 RESIDUES IN THE SEQUENCE OF MONOMER A AND FIRST 59 RESIDUES IN MONOMER B. IN BOTH MONOMERS THE ELECTRON DENSITY IS POOR FOR A SHORT LOOP RESPECTIVELY. NO MODEL COULD BE BUILT IN THIS REGION.
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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: 33.12 Å2
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Refinement step | Cycle: LAST / Resolution: 2→57.45 Å
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