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Yorodumi- PDB-6j5y: Crystal structure of fumarylpyruvate hydrolase from Pseudomonas a... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6j5y | |||||||||
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Title | Crystal structure of fumarylpyruvate hydrolase from Pseudomonas aeruginosa in complex with Mn2+ and pyruvate | |||||||||
Components | FAA hydrolase family protein | |||||||||
Keywords | HYDROLASE | |||||||||
Function / homology | Function and homology information | |||||||||
Biological species | Pseudomonas aeruginosa (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.98 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 | 6j5y.cif.gz | 61.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6j5y.ent.gz | 42.5 KB | Display | PDB format |
PDBx/mmJSON format | 6j5y.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6j5y_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 6j5y_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 6j5y_validation.xml.gz | 10.5 KB | Display | |
Data in CIF | 6j5y_validation.cif.gz | 13.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/j5/6j5y ftp://data.pdbj.org/pub/pdb/validation_reports/j5/6j5y | HTTPS FTP |
-Related structure data
Related structure data | 6j57C 6j5xC 4maqS 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: 26597.949 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: C8257_14365, PAMH19_5939 / Plasmid: pET30a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A080VH08, UniProt: Q9I111*PLUS |
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#2: Chemical | ChemComp-PYR / |
#3: Chemical | ChemComp-MN / |
#4: 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: 1.74 Å3/Da / Density % sol: 29.45 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.5 / Details: PEG300, Sodium acetate, Sodium chloride |
-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: 1.975→52.33 Å / Num. obs: 13405 / % possible obs: 94.7 % / Redundancy: 3 % / Rpim(I) all: 0.039 / Net I/σ(I): 31.877 |
Reflection shell | Resolution: 1.98→2.01 Å / Num. unique obs: 1101 / Rpim(I) all: 0.191 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4MAQ Resolution: 1.98→32.81 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.925 / SU B: 4.315 / SU ML: 0.123 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.225 / ESU R Free: 0.177 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: 65.83 Å2 / Biso mean: 25.518 Å2 / Biso min: 14.97 Å2
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Refinement step | Cycle: final / Resolution: 1.98→32.81 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.975→2.026 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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