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Yorodumi- PDB-3o7i: Crystal structure of 2-oxo-4-hydroxy-4-carboxy-5-ureidoimidazolin... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3o7i | ||||||
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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 / FOURIER SYNTHESIS / Resolution: 1.5 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 | 3o7i.cif.gz | 83.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3o7i.ent.gz | 62 KB | Display | PDB format |
PDBx/mmJSON format | 3o7i.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3o7i_validation.pdf.gz | 434.4 KB | Display | wwPDB validaton report |
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Full document | 3o7i_full_validation.pdf.gz | 435.1 KB | Display | |
Data in XML | 3o7i_validation.xml.gz | 19.3 KB | Display | |
Data in CIF | 3o7i_validation.cif.gz | 31.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/o7/3o7i ftp://data.pdbj.org/pub/pdb/validation_reports/o7/3o7i | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 20833.295 Da / Num. of mol.: 2 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 #2: 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: 1.88 Å3/Da / Density % sol: 34.44 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 20% PEG-3000, 0.2 M calcium acetate, pH 7.0 Tris-HCl, 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: 1.5→50 Å / Num. all: 49900 / Num. obs: 49800 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 7.4 % / Rsym value: 0.096 / Net I/σ(I): 28.7 |
Reflection shell | Resolution: 1.5→1.53 Å / Redundancy: 7.2 % / Mean I/σ(I) obs: 7.3 / Num. unique all: 2462 / Rsym value: 0.37 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS / Resolution: 1.5→29.39 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.926 / SU B: 1.364 / SU ML: 0.052 / Cross valid method: THROUGHOUT / ESU R Free: 0.088 / 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: 10.786 Å2
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Refinement step | Cycle: LAST / Resolution: 1.5→29.39 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.5→1.539 Å / Total num. of bins used: 20
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