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Yorodumi- PDB-3dug: Crystal structure of zn-dependent arginine carboxypeptidase compl... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3dug | ||||||
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Title | Crystal structure of zn-dependent arginine carboxypeptidase complexed with zinc | ||||||
Components | ZN-DEPENDENT ARGININE CARBOXYPEPTIDASE | ||||||
Keywords | HYDROLASE / UNKNOWN SOURCE / AMIDOHYDROLASE / SARGASSO SEA / STRUCTURAL GENOMICS / PROTEIN STRUCTURE INITIATIVE / PSI / NEW YORK STRUCTURAL GENOMIX RESEARCH CONSORTIUM / NYSGXRC / New York SGX Research Center for Structural Genomics | ||||||
Function / homology | Urease, subunit C; domain 1 / Urease, subunit C, domain 1 / Metal-dependent hydrolases / Roll / TIM Barrel / Alpha-Beta Barrel / Mainly Beta / Alpha Beta / ARGININE Function and homology information | ||||||
Biological species | unidentified (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.62 Å | ||||||
Authors | Patskovsky, Y. / Ramagopal, U.A. / Toro, R. / Meyer, A.J. / Freeman, J. / Iizuka, M. / Bain, K. / Rodgers, L. / Raushel, F. / Sauder, J.M. ...Patskovsky, Y. / Ramagopal, U.A. / Toro, R. / Meyer, A.J. / Freeman, J. / Iizuka, M. / Bain, K. / Rodgers, L. / Raushel, F. / Sauder, J.M. / Burley, S.K. / Almo, S.C. / New York SGX Research Center for Structural Genomics (NYSGXRC) | ||||||
Citation | Journal: Biochemistry / Year: 2009 Title: Functional identification of incorrectly annotated prolidases from the amidohydrolase superfamily of enzymes. Authors: Xiang, D.F. / Patskovsky, Y. / Xu, C. / Meyer, A.J. / Sauder, J.M. / Burley, S.K. / Almo, S.C. / Raushel, F.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3dug.cif.gz | 599.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3dug.ent.gz | 497.1 KB | Display | PDB format |
PDBx/mmJSON format | 3dug.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3dug_validation.pdf.gz | 543.1 KB | Display | wwPDB validaton report |
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Full document | 3dug_full_validation.pdf.gz | 586.1 KB | Display | |
Data in XML | 3dug_validation.xml.gz | 111 KB | Display | |
Data in CIF | 3dug_validation.cif.gz | 147.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/du/3dug ftp://data.pdbj.org/pub/pdb/validation_reports/du/3dug | HTTPS FTP |
-Related structure data
Related structure data | 3be7SC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: PRO / Beg label comp-ID: PRO / End auth comp-ID: ARG / End label comp-ID: ARG / Refine code: 1 / Auth seq-ID: 56 - 398 / Label seq-ID: 58 - 400
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-Components
#1: Protein | Mass: 44486.523 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) unidentified (others) #2: Chemical | ChemComp-ZN / #3: Chemical | ChemComp-ARG / #4: Chemical | ChemComp-GOL / #5: 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: 2.98 Å3/Da / Density % sol: 58.73 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 100MM SUCCINIC ACID PH 7.0, 15% PEG 3350, 5MM ZINC SULFATE, 10% GLYCEROL, VAPOR DIFFUSION, SITTING DROP, REMARK TEMPERATURE 294K, pH 7.00 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.9791 |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 21, 2007 / Details: MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9791 Å / Relative weight: 1 |
Reflection | Resolution: 2.62→50 Å / Num. obs: 127892 / % possible obs: 99.4 % / Observed criterion σ(I): -0.5 / Redundancy: 3.6 % / Rmerge(I) obs: 0.11 / Rsym value: 0.11 / Net I/σ(I): 4.1 |
Reflection shell | Resolution: 2.62→2.71 Å / Redundancy: 3 % / Rmerge(I) obs: 0.79 / Mean I/σ(I) obs: 0.7 / % possible all: 98.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3BE7 Resolution: 2.62→20 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.918 / SU B: 15.487 / SU ML: 0.293 / Cross valid method: THROUGHOUT / ESU R: 0.615 / ESU R Free: 0.313 / 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 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 75.913 Å2
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Refinement step | Cycle: LAST / Resolution: 2.62→20 Å
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Refine LS restraints |
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Refine LS restraints NCS | Ens-ID: 1 / Number: 2560 / Refine-ID: X-RAY DIFFRACTION
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LS refinement shell | Resolution: 2.62→2.687 Å / Total num. of bins used: 20
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