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Yorodumi- PDB-1y81: Conserved hypothetical protein Pfu-723267-001 from Pyrococcus furiosus -
+Open data
-Basic information
Entry | Database: PDB / ID: 1y81 | ||||||
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Title | Conserved hypothetical protein Pfu-723267-001 from Pyrococcus furiosus | ||||||
Components | conserved hypothetical protein | ||||||
Keywords | structural genomics / unknown function / conserved hypothetical protein / Pyrococcus furiosus / hyperthermophile / PSI / Protein Structure Initiative / Southeast Collaboratory for Structural Genomics / SECSG | ||||||
Function / homology | Function and homology information CoA binding domain / CoA binding domain / CoA-binding / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta Similarity search - Domain/homology | ||||||
Biological species | Pyrococcus furiosus (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAS / sad / Resolution: 1.701 Å | ||||||
Authors | Zhao, M. / Chang, J. / Habel, J. / Xu, H. / Chen, L. / Lee, D. / Nguyen, D. / Chang, S.-H. / Horanyi, P. / Florence, Q. ...Zhao, M. / Chang, J. / Habel, J. / Xu, H. / Chen, L. / Lee, D. / Nguyen, D. / Chang, S.-H. / Horanyi, P. / Florence, Q. / Tempel, W. / Zhou, W. / Lin, D. / Zhang, H. / Praissman, J. / Jenney Jr., F.E. / Adams, M.W.W. / Liu, Z.-J. / Rose, J.P. / Wang, B.-C. / Southeast Collaboratory for Structural Genomics (SECSG) | ||||||
Citation | Journal: To be published Title: Conserved hypothetical protein Pfu-723267-001 from Pyrococcus furiosus Authors: Zhao, M. / Chang, J. / Habel, J. / Xu, H. / Chen, L. / Lee, D. / Nguyen, D. / Chang, S.-H. / Horanyi, P. / Florence, Q. / Tempel, W. / Zhou, W. / Lin, D. / Zhang, H. / Praissman, J. / Jenney ...Authors: Zhao, M. / Chang, J. / Habel, J. / Xu, H. / Chen, L. / Lee, D. / Nguyen, D. / Chang, S.-H. / Horanyi, P. / Florence, Q. / Tempel, W. / Zhou, W. / Lin, D. / Zhang, H. / Praissman, J. / Jenney Jr., F.E. / Adams, M.W.W. / Liu, Z.-J. / Rose, J.P. / Wang, B.-C. | ||||||
History |
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Remark 300 | BIOMOLECULE: THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 CHAIN. ...BIOMOLECULE: THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 CHAIN. THE BIOLOGICAL UNIT IS UNKNOWN. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1y81.cif.gz | 35.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1y81.ent.gz | 25.4 KB | Display | PDB format |
PDBx/mmJSON format | 1y81.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1y81_validation.pdf.gz | 692.4 KB | Display | wwPDB validaton report |
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Full document | 1y81_full_validation.pdf.gz | 692.4 KB | Display | |
Data in XML | 1y81_validation.xml.gz | 7.2 KB | Display | |
Data in CIF | 1y81_validation.cif.gz | 8.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/y8/1y81 ftp://data.pdbj.org/pub/pdb/validation_reports/y8/1y81 | HTTPS FTP |
-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: 15661.961 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pyrococcus furiosus (archaea) / Production host: Escherichia coli (E. coli) / References: UniProt: Q8U2V3 | ||
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#2: Chemical | ChemComp-SCN / | ||
#3: Chemical | ChemComp-COA / | ||
#4: Chemical | ChemComp-UNX / #5: 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: 2.1 Å3/Da / Density % sol: 41.44 % |
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Crystal grow | Temperature: 291 K / Method: modified microbatch Details: 0.3M sodium thiocyanate, 35% w/v PEG 3350, modified microbatch, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.9791 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 26, 2004 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9791 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.59→50 Å / Num. obs: 14818 / % possible obs: 83.1 % / Rmerge(I) obs: 0.054 / Χ2: 1.424 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: sad | |||||||||||||||||||||||||||||||||||||||||||||||||
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Phasing MAD | D res high: 2.2 Å / D res low: 20 Å / FOM : 0.43 / Reflection: 6722 | |||||||||||||||||||||||||||||||||||||||||||||||||
Phasing MAD shell |
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Phasing dm | FOM : 0.66 / FOM acentric: 0.66 / FOM centric: 0.71 / Reflection: 7765 / Reflection acentric: 7127 / Reflection centric: 638 | |||||||||||||||||||||||||||||||||||||||||||||||||
Phasing dm shell |
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-Processing
Software |
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Refinement | Method to determine structure: SAS / Resolution: 1.701→68.519 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.935 / WRfactor Rfree: 0.261 / WRfactor Rwork: 0.23 / SU B: 2.468 / SU ML: 0.082 / SU R Cruickshank DPI: 0.125 / Cross valid method: THROUGHOUT / ESU R: 0.125 / ESU R Free: 0.116 / 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: MASK BULK SOLVENT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 24.266 Å2
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Refinement step | Cycle: LAST / Resolution: 1.701→68.519 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20
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