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Yorodumi- PDB-6j57: Crystal structure of fumarylpyruvate hydrolase from Corynebacteri... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6j57 | ||||||
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Title | Crystal structure of fumarylpyruvate hydrolase from Corynebacterium glutamicum | ||||||
Components | Predicted 2-keto-4-pentenoate hydratase/2-oxohepta-3-ene-1,7-dioic acid hydratase | ||||||
Keywords | HYDROLASE | ||||||
Function / homology | Function and homology information Lyases; Carbon-carbon lyases; Carboxy-lyases / Isomerases; Intramolecular oxidoreductases; Transposing C=C bonds / catalytic activity / isomerase activity / lyase activity Similarity search - Function | ||||||
Biological species | Corynebacterium glutamicum (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.01 Å | ||||||
Authors | Hong, H. / Seo, H. / Kim, K.-J. / Park, W. | ||||||
Citation | Journal: Environ.Microbiol. / Year: 2020 Title: Sequence, structure and function-based classification of the broadly conserved FAH superfamily reveals two distinct fumarylpyruvate hydrolase subfamilies. Authors: Hong, H. / Seo, H. / Park, W. / Kim, K.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6j57.cif.gz | 124.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6j57.ent.gz | 97.2 KB | Display | PDB format |
PDBx/mmJSON format | 6j57.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/j5/6j57 ftp://data.pdbj.org/pub/pdb/validation_reports/j5/6j57 | HTTPS FTP |
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-Related structure data
Related structure data | 6j5xC 6j5yC 3rr6S 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
#1: Protein | Mass: 31659.410 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Corynebacterium glutamicum (bacteria) / Gene: cg3350 / Plasmid: pET30a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A1R4GQY2, UniProt: Q8NLC0*PLUS #2: Chemical | ChemComp-SO4 / #3: Chemical | #4: Chemical | #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: 2.26 Å3/Da / Density % sol: 45.69 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: Ammonium sulfate, HEPES |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.97934 Å |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: May 4, 2016 |
Radiation | Monochromator: Double Crystal Monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97934 Å / Relative weight: 1 |
Reflection | Resolution: 2→61.72 Å / Num. obs: 38656 / % possible obs: 98.5 % / Redundancy: 3.4 % / Rpim(I) all: 0.057 / Net I/σ(I): 19.04 |
Reflection shell | Resolution: 2→2.03 Å / Num. unique obs: 1864 / Rpim(I) all: 0.203 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3RR6 Resolution: 2.01→28.03 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.925 / SU B: 4.007 / SU ML: 0.109 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.174 / ESU R Free: 0.158 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 86.75 Å2 / Biso mean: 22.14 Å2 / Biso min: 10.68 Å2
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Refinement step | Cycle: final / Resolution: 2.01→28.03 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.006→2.058 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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