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Yorodumi- PDB-2a1v: Crystal structure of Deinococcus radiodurans protein DR2400, Pfam... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2a1v | ||||||
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Title | Crystal structure of Deinococcus radiodurans protein DR2400, Pfam domain DUF419 | ||||||
Components | conserved hypothetical protein | ||||||
Keywords | STRUCTURAL GENOMICS / UNKNOWN FUNCTION / PSI / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC | ||||||
Function / homology | Aspartate Aminotransferase, domain 1 - #30 / Uncharacterised protein YjbR / YjbR-like superfamily / YjbR / Aspartate Aminotransferase, domain 1 / Alpha-Beta Complex / Alpha Beta / Uncharacterized protein Function and homology information | ||||||
Biological species | Deinococcus radiodurans (radioresistant) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.15 Å | ||||||
Authors | Ramagopal, U.A. / Patskovsky, Y.V. / Almo, S.C. / Burley, S.K. / New York SGX Research Center for Structural Genomics (NYSGXRC) | ||||||
Citation | Journal: To be Published Title: Hypothetical protein from Deinococcus radiodurans Authors: Ramagopal, U.A. / Patskovsky, Y.V. / Almo, S.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2a1v.cif.gz | 42.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2a1v.ent.gz | 30.4 KB | Display | PDB format |
PDBx/mmJSON format | 2a1v.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a1/2a1v ftp://data.pdbj.org/pub/pdb/validation_reports/a1/2a1v | 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: 16303.494 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Deinococcus radiodurans (radioresistant) Production host: Escherichia coli (E. coli) / References: UniProt: Q9RRT5 |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.2 Å3/Da / Density % sol: 44 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: PEG 3350, Sodium formate 0.2 M, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X9A / Wavelength: 0.98 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Jan 20, 2005 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 2.15→20 Å / Num. all: 7775 / Num. obs: 7775 / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.9 % / Rmerge(I) obs: 0.094 / Rsym value: 0.071 / Net I/σ(I): 22.6 |
Reflection shell | Resolution: 2.15→2.23 Å / Redundancy: 7.5 % / Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 4.1 / Rsym value: 0.46 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.15→20 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.913 / SU B: 5.538 / SU ML: 0.145 / Cross valid method: THROUGHOUT / ESU R: 0.26 / 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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.714 Å2
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Refinement step | Cycle: LAST / Resolution: 2.15→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.15→2.178 Å / Total num. of bins used: 40
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