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Yorodumi- PDB-3o7j: Crystal structure of 2-oxo-4-hydroxy-4-carboxy-5-ureidoimidazolin... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3o7j | ||||||
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Title | Crystal structure of 2-oxo-4-hydroxy-4-carboxy-5-ureidoimidazoline decarboxylase from Klebsiella pneumoniae | ||||||
Components | OHCU decarboxylase | ||||||
Keywords | LYASE / decarboxylase | ||||||
Function / homology | Function and homology information 2-oxo-4-hydroxy-4-carboxy-5-ureidoimidazoline decarboxylase activity / 2-oxo-4-hydroxy-4-carboxy-5-ureidoimidazoline decarboxylase / urate catabolic process / purine nucleobase metabolic process / peroxisome Similarity search - Function | ||||||
Biological species | Klebsiella pneumoniae subsp. pneumoniae (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | French, J.B. / Ealick, S.E. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2010 Title: Structural and Mechanistic Studies on Klebsiella pneumoniae 2-Oxo-4-hydroxy-4-carboxy-5-ureidoimidazoline Decarboxylase. Authors: French, J.B. / Ealick, S.E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3o7j.cif.gz | 47.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3o7j.ent.gz | 32.4 KB | Display | PDB format |
PDBx/mmJSON format | 3o7j.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3o7j_validation.pdf.gz | 444.8 KB | Display | wwPDB validaton report |
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Full document | 3o7j_full_validation.pdf.gz | 444.8 KB | Display | |
Data in XML | 3o7j_validation.xml.gz | 9.2 KB | Display | |
Data in CIF | 3o7j_validation.cif.gz | 12.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/o7/3o7j ftp://data.pdbj.org/pub/pdb/validation_reports/o7/3o7j | HTTPS FTP |
-Related structure data
Related structure data | 3o7hC 3o7iC 3o7kC 2q37S C: citing same article (ref.) S: Starting model for refinement |
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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: 20833.295 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Klebsiella pneumoniae subsp. pneumoniae (bacteria) Strain: ATCC 700721 / Gene: KPN78578_16350, KPN_01665 / Production host: Escherichia coli (E. coli) / References: UniProt: A6T925 |
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#2: Chemical | ChemComp-2AL / |
#3: 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: 2.18 Å3/Da / Density % sol: 43.5 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 22-26% PEG-8000, 0.25 M sodium acetate in pH 6.5 cacodylate, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.987 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Jan 1, 2010 |
Radiation | Monochromator: Horizontal focusing 5.05 asymmetric cut Si(111) Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.987 Å / Relative weight: 1 |
Reflection | Resolution: 2→50 Å / Num. all: 12300 / Num. obs: 12100 / % possible obs: 98.6 % / Observed criterion σ(I): 2 / Redundancy: 2.4 % / Rsym value: 0.076 / Net I/σ(I): 16.5 |
Reflection shell | Resolution: 2→2.03 Å / Redundancy: 2 % / Mean I/σ(I) obs: 2.6 / Num. unique all: 560 / Rsym value: 0.263 / % possible all: 94.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2Q37 Resolution: 2→25.61 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.915 / SU B: 4.809 / SU ML: 0.135 / Cross valid method: THROUGHOUT / ESU R Free: 0.171 / 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: 25.162 Å2
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Refinement step | Cycle: LAST / Resolution: 2→25.61 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.05 Å / Total num. of bins used: 20
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