+Open data
-Basic information
Entry | Database: PDB / ID: 3qva | ||||||
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Title | Structure of Klebsiella pneumoniae 5-hydroxyisourate hydrolase | ||||||
Components | Transthyretin-like protein | ||||||
Keywords | HYDROLASE / Transthyretin-related protein / 5-hydroxyisourate hydrolase | ||||||
Function / homology | Function and homology information hydroxyisourate hydrolase / hydroxyisourate hydrolase activity / purine nucleobase metabolic process Similarity search - Function | ||||||
Biological species | Klebsiella pneumoniae subsp. pneumoniae (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.755 Å | ||||||
Authors | French, J.B. / Ealick, S.E. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2011 Title: Structural and kinetic insights into the mechanism of 5-hydroxyisourate hydrolase from Klebsiella pneumoniae. 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 | 3qva.cif.gz | 96.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3qva.ent.gz | 72.9 KB | Display | PDB format |
PDBx/mmJSON format | 3qva.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3qva_validation.pdf.gz | 468 KB | Display | wwPDB validaton report |
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Full document | 3qva_full_validation.pdf.gz | 474 KB | Display | |
Data in XML | 3qva_validation.xml.gz | 20 KB | Display | |
Data in CIF | 3qva_validation.cif.gz | 28.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qv/3qva ftp://data.pdbj.org/pub/pdb/validation_reports/qv/3qva | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 12441.810 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Klebsiella pneumoniae subsp. pneumoniae (bacteria) Strain: ATCC 700721 / MGH 78578 / Gene: HpxT, KPN78578_16360, KPN_01666 / Plasmid: Pet28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: A6T926 #2: Chemical | #3: 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: 2.28 Å3/Da / Density % sol: 46.01 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop Details: 0.1M imidazole pH 7.5-8.5, 0.5 - 1.0 M ammonium phosphate, VAPOR DIFFUSION, HANGING DROP, temperature 291K PH range: 7.5-8.5 |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.979 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 15, 2009 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: focusing mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.755→73.272 Å / Num. all: 45752 / Num. obs: 45752 / % possible obs: 99.4 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 4.8 % / Rmerge(I) obs: 0.044 / Χ2: 1.229 / Net I/σ(I): 18.2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.755→73.27 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.938 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 2.122 / SU ML: 0.07 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.122 / ESU R Free: 0.113 / Stereochemistry target values: MAXIMUM LIKELIHOOD 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: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 57.18 Å2 / Biso mean: 18.8049 Å2 / Biso min: 8.74 Å2
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Refinement step | Cycle: LAST / Resolution: 1.755→73.27 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.755→1.801 Å / Total num. of bins used: 20
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