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Yorodumi- PDB-4ea8: X-ray crystal structure of PerB from Caulobacter crescentus in co... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4ea8 | ||||||
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Title | X-ray crystal structure of PerB from Caulobacter crescentus in complex with coenzyme A and GDP-N-acetylperosamine at 1 Angstrom resolution | ||||||
Components | Perosamine N-acetyltransferase | ||||||
Keywords | TRANSFERASE / beta helix / acetyltransferase / acetyl coenzyme A / GDP-perosamine | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Caulobacter vibrioides (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1 Å | ||||||
Authors | Thoden, J.B. / Reinhardt, L.A. / Cook, P.D. / Menden, P. / Cleland, W.W. / Holden, H.M. | ||||||
Citation | Journal: Biochemistry / Year: 2012 Title: Catalytic Mechanism of Perosamine N-Acetyltransferase Revealed by High-Resolution X-ray Crystallographic Studies and Kinetic Analyses. Authors: Thoden, J.B. / Reinhardt, L.A. / Cook, P.D. / Menden, P. / Cleland, W.W. / 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 | 4ea8.cif.gz | 111.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4ea8.ent.gz | 84 KB | Display | PDB format |
PDBx/mmJSON format | 4ea8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ea/4ea8 ftp://data.pdbj.org/pub/pdb/validation_reports/ea/4ea8 | HTTPS FTP |
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-Related structure data
Related structure data | 4ea7SC 4ea9C 4eaaC 4eabC 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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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 21910.334 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Caulobacter vibrioides (bacteria) / Gene: CC_1011, wbqR / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2(DE3) References: UniProt: O85353, Transferases; Acyltransferases; Transferring groups other than aminoacyl groups | ||
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#2: Chemical | ChemComp-COA / | ||
#3: Chemical | ChemComp-JB3 / | ||
#4: Chemical | #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: 2.93 Å3/Da / Density % sol: 57.98 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 25-30% PEG5000 MME, 100 mM HEPES, pH 7.5, 5 mM CoA, 5 mM GDP, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.667 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 19, 2009 |
Radiation | Monochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.667 Å / Relative weight: 1 |
Reflection | Resolution: 1→50 Å / Num. all: 132601 / Num. obs: 132601 / % possible obs: 98.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.2 % / Rmerge(I) obs: 0.063 / Rsym value: 0.063 / Net I/σ(I): 47.1 |
Reflection shell | Resolution: 1→1.02 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.391 / Mean I/σ(I) obs: 2 / Num. unique all: 6425 / Rsym value: 0.391 / % possible all: 95.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4EA7 Resolution: 1→50 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 1→50 Å
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