+Open data
-Basic information
Entry | Database: PDB / ID: 2yzv | ||||||
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Title | ADP-ribosylglycohydrolase-related protein complex | ||||||
Components | ADP-ribosylglycohydrolaseADP-ribosylhydrolase | ||||||
Keywords | HYDROLASE / All alpha protein / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI | ||||||
Function / homology | ADP-ribosylglycohydrolase fold / ADP-ribosylation/Crystallin J1 / ADP-ribosylation/Crystallin J1 / ADP-ribosylglycohydrolase / ADP-ribosylation/Crystallin J1 superfamily / Orthogonal Bundle / Mainly Alpha / metal ion binding / ADP-ribosylglycohydrolase Function and homology information | ||||||
Biological species | Thermus thermophilus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å | ||||||
Authors | Ebihara, A. / Manzoku, M. / Yokoyama, S. / Kuramitsu, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
Citation | Journal: To be Published Title: ADP-ribosylglycohydrolase-related protein complex Authors: Ebihara, A. / Manzoku, M. / Yokoyama, S. / Kuramitsu, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2yzv.cif.gz | 72.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2yzv.ent.gz | 52.1 KB | Display | PDB format |
PDBx/mmJSON format | 2yzv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yz/2yzv ftp://data.pdbj.org/pub/pdb/validation_reports/yz/2yzv | HTTPS FTP |
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-Related structure data
Related structure data | 2yzwC 2cwcS 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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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 32955.500 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB8 / Plasmid: pET-11a / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta(DE3) / References: UniProt: Q5SMG9 | ||
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#2: Chemical | #3: 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: 1.92 Å3/Da / Density % sol: 35.93 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.2 Details: 0.1M Lithium chloride, 0.1M Tris-HCl; crystal soaking with MgCl2, pH 8.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B2 / Wavelength: 1 Å |
Detector | Type: RIGAKU JUPITER 210 / Detector: CCD / Date: Oct 20, 2006 |
Radiation | Monochromator: SI Double-Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→50 Å / Num. obs: 34370 / % possible obs: 99.9 % / Redundancy: 6.6 % / Biso Wilson estimate: 17.5 Å2 / Rmerge(I) obs: 0.063 / Net I/σ(I): 32.8 |
Reflection shell | Resolution: 1.6→1.66 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.2 / Mean I/σ(I) obs: 4.07 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2CWC Resolution: 1.6→34.53 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 1090474.84 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 41.6895 Å2 / ksol: 0.361531 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 18.6 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.6→34.53 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.6→1.7 Å / Rfactor Rfree error: 0.011 / Total num. of bins used: 6
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Xplor file |
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