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Yorodumi- PDB-3rp6: Crystal Structure of Klebsiella pneumoniae HpxO complexed with FAD -
+Open data
-Basic information
Entry | Database: PDB / ID: 3rp6 | ||||||
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Title | Crystal Structure of Klebsiella pneumoniae HpxO complexed with FAD | ||||||
Components | flavoprotein monooxygenase | ||||||
Keywords | OXIDOREDUCTASE / FAD-binding protein / monooxygenase | ||||||
Function / homology | Function and homology information FAD-dependent urate hydroxylase / FAD-dependent urate hydroxylase activity / oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, NAD(P)H as one donor, and incorporation of one atom of oxygen / urate oxidase activity / urate catabolic process / purine nucleobase metabolic process / FAD binding Similarity search - Function | ||||||
Biological species | Klebsiella pneumoniae (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.2 Å | ||||||
Authors | Hicks, K.A. / O'Leary, S.E. / Begley, T.P. / Ealick, S.E. | ||||||
Citation | Journal: Biochemistry / Year: 2013 Title: Structural and Mechanistic Studies of HpxO, a Novel Flavin Adenine Dinucleotide-Dependent Urate Oxidase from Klebsiella pneumoniae. Authors: Hicks, K.A. / O'Leary, S.E. / Begley, T.P. / 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 | 3rp6.cif.gz | 86.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3rp6.ent.gz | 68.2 KB | Display | PDB format |
PDBx/mmJSON format | 3rp6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3rp6_validation.pdf.gz | 699 KB | Display | wwPDB validaton report |
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Full document | 3rp6_full_validation.pdf.gz | 701.8 KB | Display | |
Data in XML | 3rp6_validation.xml.gz | 16.3 KB | Display | |
Data in CIF | 3rp6_validation.cif.gz | 22.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rp/3rp6 ftp://data.pdbj.org/pub/pdb/validation_reports/rp/3rp6 | HTTPS FTP |
-Related 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: 45401.504 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Strain: ATCC 700721 / MGH 78578 / Gene: KPN78578_16330, KPN_01663 / Plasmid: modified pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3) / References: UniProt: A6T923 |
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#2: Chemical | ChemComp-FAD / |
#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: 2.04 Å3/Da / Density % sol: 39.59 % |
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Crystal grow | Temperature: 291 K / Method: hanging drop Details: 0.05 M KH2PO4, 20% PEG 8000, hanging drop, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 18, 2009 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Cryo-Cooled Si(111) double crystal / Protocol: SINGLE WAVELENGTH / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.2→50 Å / Num. all: 19184 / Num. obs: 19184 / % possible obs: 98.4 % / Observed criterion σ(I): -3 / Redundancy: 8.2 % / Rmerge(I) obs: 0.1 / Χ2: 1.49 / Net I/σ(I): 10.5 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.2→34.925 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8282 / SU ML: 0.22 / σ(F): 1.36 / Phase error: 23.85 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 34.894 Å2 / ksol: 0.36 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 70.97 Å2 / Biso mean: 35.654 Å2 / Biso min: 18.32 Å2
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Refinement step | Cycle: LAST / Resolution: 2.2→34.925 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 7
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