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Yorodumi- PDB-3r03: The crystal structure of NUDIX hydrolase from Rhodospirillum rubrum -
+Open data
-Basic information
Entry | Database: PDB / ID: 3r03 | ||||||
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Title | The crystal structure of NUDIX hydrolase from Rhodospirillum rubrum | ||||||
Components | NUDIX hydrolase | ||||||
Keywords | HYDROLASE / Structural Genomics / PSI2 / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Rhodospirillum rubrum (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.491 Å | ||||||
Authors | Zhang, Z. / Burley, S.K. / Swaminathan, S. / New York SGX Research Center for Structural Genomics (NYSGXRC) | ||||||
Citation | Journal: To be Published Title: The crystal structure of NUDIX hydrolase from Rhodospirillum rubrum Authors: Zhang, Z. / Burley, S.K. / Swaminathan, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3r03.cif.gz | 59.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3r03.ent.gz | 47.7 KB | Display | PDB format |
PDBx/mmJSON format | 3r03.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/r0/3r03 ftp://data.pdbj.org/pub/pdb/validation_reports/r0/3r03 | 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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Details | THE AUTHOR STATES THAT THE BIOLOGICAL UNIT OF THIS PROTEIN IS UNKNOWN. |
-Components
#1: Protein | Mass: 16082.025 Da / Num. of mol.: 2 / Fragment: sequence database residues 18-151 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rhodospirillum rubrum (bacteria) / Strain: strain ATCC 11170 / Gene: Rru_A0393 / Plasmid: BC-pSGX3 (BC) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-codon+RIL(p) / References: UniProt: Q2RXE7 #2: Chemical | ChemComp-ADP / | #3: 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: 2.61 Å3/Da / Density % sol: 52.83 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.6 Details: 0.1 M Sodium acetate trihydarate pH 4.6, 8% PEG 4000, 10 mM ATP, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 0.9795 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jan 1, 2011 / Details: mirrors |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 2.49→50 Å / Num. obs: 11862 / % possible obs: 99.07 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 22 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 27.1 |
Reflection shell | Resolution: 2.49→2.58 Å / Redundancy: 21 % / Rmerge(I) obs: 0.41 / Mean I/σ(I) obs: 5.7 / Num. unique all: 1178 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.491→46.534 Å / SU ML: 0.43 / Isotropic thermal model: Isotropic / σ(F): 5.05 / Phase error: 29.54 / Stereochemistry target values: Engh & Huber
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40.27 Å2 / ksol: 0.314 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.491→46.534 Å
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Refine LS restraints |
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LS refinement shell |
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