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Yorodumi- PDB-4uw9: The crystal structural of archaeal beta-phosphoglucomutase from h... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4uw9 | ||||||
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Title | The crystal structural of archaeal beta-phosphoglucomutase from hyper-thermophilic Pyrococcus sp. Strain ST 04 | ||||||
Components | BETA-PHOSPHOGLUCOMUTASE | ||||||
Keywords | ISOMERASE / ARCHAEAL PHOSPHOGLUCOMUTASE | ||||||
Function / homology | Function and homology information Haloacid dehalogenase-like hydrolase / Haloacid dehalogenase-like hydrolase / Putative phosphatase; domain 2 / Phosphoglycolate phosphatase-like, domain 2 / HAD superfamily/HAD-like / HAD superfamily / HAD-like superfamily / DNA polymerase; domain 1 / Rossmann fold / Orthogonal Bundle ...Haloacid dehalogenase-like hydrolase / Haloacid dehalogenase-like hydrolase / Putative phosphatase; domain 2 / Phosphoglycolate phosphatase-like, domain 2 / HAD superfamily/HAD-like / HAD superfamily / HAD-like superfamily / DNA polymerase; domain 1 / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta Similarity search - Domain/homology | ||||||
Biological species | PYROCOCCUS SP. ST04 (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.3 Å | ||||||
Authors | Park, K.-H. / Woo, E.-J. | ||||||
Citation | Journal: To be Published Title: Structural Features of Archaeal Beta-Phosphoglucomutase from Hyper-Thermophilic Pyrococcus Sp. Strain St 04 Authors: Park, K.-H. / Jung, J.-H. / Park, C.-S. / Woo, E.-J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4uw9.cif.gz | 55.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4uw9.ent.gz | 43.9 KB | Display | PDB format |
PDBx/mmJSON format | 4uw9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4uw9_validation.pdf.gz | 422.3 KB | Display | wwPDB validaton report |
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Full document | 4uw9_full_validation.pdf.gz | 423.6 KB | Display | |
Data in XML | 4uw9_validation.xml.gz | 11.4 KB | Display | |
Data in CIF | 4uw9_validation.cif.gz | 15.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/uw/4uw9 ftp://data.pdbj.org/pub/pdb/validation_reports/uw/4uw9 | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 25991.385 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) PYROCOCCUS SP. ST04 (archaea) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: I3RFR5 |
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#2: Chemical | ChemComp-MG / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 3.59 Å3/Da / Density % sol: 65.7 % / Description: NONE |
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-Data collection
Diffraction | Mean temperature: 95 K |
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 1 |
Detector | Type: ADSC CCD / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→31.22 Å / Num. obs: 16290 / % possible obs: 99 % / Observed criterion σ(I): 6.6 / Redundancy: 6 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 43.67 |
-Processing
Software | Name: PHENIX / Version: (PHENIX.REFINE: 1.8.4_1496) / Classification: refinement | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: SAD Starting model: NONE Resolution: 2.3→31.225 Å / SU ML: 0.24 / σ(F): 1.17 / Phase error: 22.12 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→31.225 Å
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Refine LS restraints |
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LS refinement shell |
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