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Yorodumi- PDB-4j7h: Crystal structure of EvaA, a 2,3-dehydratase in complex with dTDP... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4j7h | ||||||
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Title | Crystal structure of EvaA, a 2,3-dehydratase in complex with dTDP-benzene and dTDP-rhamnose | ||||||
Components | EvaA 2,3-dehydratase | ||||||
Keywords | BIOSYNTHETIC PROTEIN / Nudix hydrolase superfamily / dehydration | ||||||
Function / homology | Function and homology information dTDP-4-dehydro-6-deoxy-alpha-D-glucopyranose 2,3-dehydratase / antibiotic biosynthetic process / lyase activity Similarity search - Function | ||||||
Biological species | Amycolatopsis orientalis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.69 Å | ||||||
Authors | Holden, H.M. / Kubiak, R.L. / Thoden, J.B. | ||||||
Citation | Journal: Biochemistry / Year: 2013 Title: Structure of EvaA: A Paradigm for Sugar 2,3-Dehydratases. Authors: Kubiak, R.L. / Thoden, J.B. / 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 | 4j7h.cif.gz | 207.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4j7h.ent.gz | 171.9 KB | Display | PDB format |
PDBx/mmJSON format | 4j7h.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/j7/4j7h ftp://data.pdbj.org/pub/pdb/validation_reports/j7/4j7h | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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2 |
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3 |
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Unit cell |
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-Components
#1: Protein | Mass: 53000.762 Da / Num. of mol.: 2 / Mutation: R381A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Amycolatopsis orientalis (bacteria) / Strain: NRRL 18098 / Gene: EvaA / Plasmid: pET-28JT / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2 (DE3) / References: UniProt: O52793 #2: Chemical | #3: Chemical | #4: Chemical | ChemComp-EDO / #5: 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: 2.95 Å3/Da / Density % sol: 58.36 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 20% PEG 8000, 100 mM HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.979 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 9, 2012 |
Radiation | Monochromator: double crystal monochromator Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 1.69→110.13 Å / Num. all: 135159 / Num. obs: 135159 / % possible obs: 97.2 % / Redundancy: 7 % / Rsym value: 0.054 / Net I/σ(I): 55.7 |
Reflection shell | Resolution: 1.7→1.86 Å / Redundancy: 3.5 % / Mean I/σ(I) obs: 6.3 / Num. unique all: 12455 / % possible all: 90.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.69→110.13 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.954 / SU B: 1.439 / SU ML: 0.049 / Cross valid method: THROUGHOUT / ESU R: 0.084 / ESU R Free: 0.084 / 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: 22.434 Å2
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Refinement step | Cycle: LAST / Resolution: 1.69→110.13 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.694→1.738 Å / Total num. of bins used: 20
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