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Yorodumi- PDB-3dr4: GDP-perosamine synthase K186A mutant from Caulobacter crescentus ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3dr4 | ||||||
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Title | GDP-perosamine synthase K186A mutant from Caulobacter crescentus with bound sugar ligand | ||||||
Components | Putative perosamine synthetase | ||||||
Keywords | TRANSFERASE / Perosamine / deoxysugar / pyridoxal phosphate / aspartate aminotransferase / o-antigen | ||||||
Function / homology | Function and homology information GDP-perosamine synthase / GDP-4-dehydro-6-deoxy-D-mannose-4-aminotransferase activity / O antigen biosynthetic process / pyridoxal phosphate binding Similarity search - Function | ||||||
Biological species | Caulobacter crescentus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å | ||||||
Authors | Holden, H.M. / Cook, P.D. / Carney, A.E. | ||||||
Citation | Journal: Biochemistry / Year: 2008 Title: Accommodation of GDP-linked sugars in the active site of GDP-perosamine synthase Authors: Cook, P.D. / Carney, A.E. / Holden, H.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3dr4.cif.gz | 326.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3dr4.ent.gz | 259.6 KB | Display | PDB format |
PDBx/mmJSON format | 3dr4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3dr4_validation.pdf.gz | 1.8 MB | Display | wwPDB validaton report |
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Full document | 3dr4_full_validation.pdf.gz | 1.8 MB | Display | |
Data in XML | 3dr4_validation.xml.gz | 70.9 KB | Display | |
Data in CIF | 3dr4_validation.cif.gz | 101.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dr/3dr4 ftp://data.pdbj.org/pub/pdb/validation_reports/dr/3dr4 | HTTPS FTP |
-Related structure data
Related structure data | 3dr7C 3bn1S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 42980.969 Da / Num. of mol.: 4 / Mutation: K186A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Caulobacter crescentus (bacteria) / Strain: CB15 / Gene: per / Plasmid: pET28T / Production host: Escherichia coli (E. coli) / Strain (production host): HMS174 / References: UniProt: O85354, UniProt: Q9A9H3*PLUS #2: Chemical | ChemComp-G4M / [( #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: 2.29 Å3/Da / Density % sol: 46.26 % |
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Crystal grow | Temperature: 298 K / Method: batch / pH: 6.5 Details: 50 mM MES, 10% PEG 8000, 1 mM PLP, 1mM glutamate, pH 6.5, batch, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97 Å |
Detector | Type: SBC-3 / Detector: CCD / Date: Feb 8, 2008 |
Radiation | Monochromator: Si-111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→50 Å / Num. all: 202983 / Num. obs: 186452 / % possible obs: 91.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 6.3 % / Rsym value: 0.041 / Net I/σ(I): 11.5 |
Reflection shell | Resolution: 1.6→1.66 Å / Redundancy: 4.6 % / Mean I/σ(I) obs: 7.6 / Num. unique all: 16930 / Rsym value: 0.214 / % possible all: 83.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 3bn1 Resolution: 1.6→26.2 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 1.6→26.2 Å
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Refine LS restraints |
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