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Yorodumi- PDB-1rpn: Crystal Structure of GDP-D-mannose 4,6-dehydratase in complexes w... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1rpn | ||||||
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Title | Crystal Structure of GDP-D-mannose 4,6-dehydratase in complexes with GDP and NADPH | ||||||
Components | GDP-mannose 4,6-dehydratase | ||||||
Keywords | LYASE / short-chain dehydrogenase/reductase / Rossmann fold | ||||||
Function / homology | Function and homology information GDP-D-rhamnose biosynthetic process / GDP-mannose 4,6-dehydratase / GDP-mannose 4,6-dehydratase activity / GDP-mannose metabolic process / 'de novo' GDP-L-fucose biosynthetic process / O antigen biosynthetic process / lipopolysaccharide biosynthetic process / NADP+ binding / cytoplasm Similarity search - Function | ||||||
Biological species | Pseudomonas aeruginosa (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å | ||||||
Authors | Webb, N.A. / Mulichak, A.M. / Lam, J.S. / Rocchetta, H.L. / Garavito, R.M. | ||||||
Citation | Journal: Protein Sci. / Year: 2004 Title: Crystal structure of a tetrameric GDP-D-mannose 4,6-dehydratase from a bacterial GDP-D-rhamnose biosynthetic pathway. Authors: Webb, N.A. / Mulichak, A.M. / Lam, J.S. / Rocchetta, H.L. / Garavito, R.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1rpn.cif.gz | 279.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1rpn.ent.gz | 224 KB | Display | PDB format |
PDBx/mmJSON format | 1rpn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rp/1rpn ftp://data.pdbj.org/pub/pdb/validation_reports/rp/1rpn | HTTPS FTP |
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-Related structure data
Related structure data | 1n7hS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 37849.805 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: GCA, PA5453 / Plasmid: pQE30 / Production host: Escherichia coli (E. coli) / Strain (production host): M15 / References: UniProt: Q51366, GDP-mannose 4,6-dehydratase #2: Chemical | ChemComp-NDP / #3: Chemical | ChemComp-GDP / #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: 3.31 Å3/Da / Density % sol: 62.9 % | |||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: MPD, Tris, ammonium phosphate, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K | |||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop | |||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 5ID-B / Wavelength: 1 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Apr 13, 2002 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.15→30 Å / Num. all: 110070 / Num. obs: 108095 / % possible obs: 98.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 5 % / Rsym value: 0.039 / Net I/σ(I): 20 |
Reflection shell | Resolution: 2.15→2.23 Å / Redundancy: 4 % / Num. unique all: 10063 / Rsym value: 0.079 / % possible all: 92.8 |
Reflection | *PLUS Highest resolution: 2.2 Å / Rmerge(I) obs: 0.039 |
Reflection shell | *PLUS % possible obs: 92.8 % / Rmerge(I) obs: 0.076 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1N7H Resolution: 2.15→30 Å / Cross valid method: THROUGHOUT / σ(F): 1 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 20.8 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.15→30 Å
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Refine LS restraints |
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Refinement | *PLUS Highest resolution: 2.2 Å / Num. reflection obs: 110170 / % reflection Rfree: 4.9 % / Rfactor Rfree: 0.195 / Rfactor Rwork: 0.173 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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