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Yorodumi- PDB-2z1m: Crystal Structure of GDP-D-Mannose Dehydratase from Aquifex aeoli... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2z1m | ||||||
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Title | Crystal Structure of GDP-D-Mannose Dehydratase from Aquifex aeolicus VF5 | ||||||
Components | GDP-D-mannose dehydratase | ||||||
Keywords | LYASE / SHORT-CHAIN DEHYDROGENASE/REDUCTASE / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI | ||||||
Function / homology | Function and homology information GDP-mannose 4,6-dehydratase / GDP-mannose 4,6-dehydratase activity / GDP-mannose metabolic process / 'de novo' GDP-L-fucose biosynthetic process / NADP+ binding Similarity search - Function | ||||||
Biological species | Aquifex aeolicus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Niwa, H. / Kuramitsu, S. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
Citation | Journal: To be Published Title: Crystal Structure of GDP-D-Mannose Dehydratase from Aquifex aeolicus VF5 Authors: Niwa, H. / Kuramitsu, S. / Yokoyama, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2z1m.cif.gz | 284.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2z1m.ent.gz | 228.4 KB | Display | PDB format |
PDBx/mmJSON format | 2z1m.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/z1/2z1m ftp://data.pdbj.org/pub/pdb/validation_reports/z1/2z1m | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 39387.094 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Aquifex aeolicus (bacteria) / Strain: VF5 / Gene: rfbD / Plasmid: pET-21a / Production host: Escherichia coli (E. coli) / References: UniProt: O67175, GDP-mannose 4,6-dehydratase #2: Chemical | #3: Chemical | #4: 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: 2.3 Å3/Da / Density % sol: 46.46 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.2 Details: 0.2M Sodium chloride , 0.1M NA/K PHOSPHATE, 40% PEG 400, pH 6.2, VAPOR DIFFUSION, SITTING 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 14, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2→50 Å / Num. all: 94553 / Num. obs: 94553 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.9 % / Biso Wilson estimate: 24.4 Å2 / Rmerge(I) obs: 0.074 / Net I/σ(I): 19.6 |
Reflection shell | Resolution: 2→2.07 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.209 / Mean I/σ(I) obs: 5.4 / Num. unique all: 8849 / % possible all: 93 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→50 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.926 / SU B: 4.002 / SU ML: 0.114 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.205 / ESU R Free: 0.17 / 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: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 26.383 Å2
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Refinement step | Cycle: LAST / Resolution: 2→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.052 Å / Total num. of bins used: 20
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