+Open data
-Basic information
Entry | Database: PDB / ID: 3qvk | ||||||
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Title | Allantoin racemase from Klebsiella pneumoniae | ||||||
Components | Putative hydantoin racemase | ||||||
Keywords | ISOMERASE / Allantoin Racemase | ||||||
Function / homology | Rossmann fold - #12500 / racemase activity, acting on amino acids and derivatives / Asp/Glu/hydantoin racemase / Asp/Glu/Hydantoin racemase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / 1-(2,5-DIOXO-2,5-DIHYDRO-1H-IMIDAZOL-4-YL)UREA / Hydantoin racemase Function and homology information | ||||||
Biological species | Klebsiella pneumoniae subsp. pneumoniae (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.999 Å | ||||||
Authors | French, J.B. / Neau, D.B. / Ealick, S.E. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2011 Title: Characterization of the Structure and Function of Klebsiella pneumoniae Allantoin Racemase. Authors: French, J.B. / Neau, D.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 | 3qvk.cif.gz | 104.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3qvk.ent.gz | 81 KB | Display | PDB format |
PDBx/mmJSON format | 3qvk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3qvk_validation.pdf.gz | 447.5 KB | Display | wwPDB validaton report |
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Full document | 3qvk_full_validation.pdf.gz | 450.1 KB | Display | |
Data in XML | 3qvk_validation.xml.gz | 22 KB | Display | |
Data in CIF | 3qvk_validation.cif.gz | 31.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qv/3qvk ftp://data.pdbj.org/pub/pdb/validation_reports/qv/3qvk | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 25567.549 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Klebsiella pneumoniae subsp. pneumoniae (bacteria) Strain: ATCC 700721 / MGH 78578 / Gene: HpxA, KPN78578_17580, KPN_01788 / Production host: Escherichia coli (E. coli) / References: UniProt: A6T9E8 #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: 2.8 Å3/Da / Density % sol: 56 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 3.9 Details: 30% Peg 400, 0.1 M sodium acetate pH 3.9, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9791 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 5, 2009 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: CRYO-COOLED SI(111) DOUBLECRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9791 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.999→108.163 Å / Num. all: 39452 / Num. obs: 39452 / % possible obs: 98.3 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 5 % / Rmerge(I) obs: 0.096 / Χ2: 2.498 / Net I/σ(I): 13.3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS / Resolution: 1.999→108.16 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.933 / Occupancy max: 1 / Occupancy min: 0.45 / SU B: 4.029 / SU ML: 0.113 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.191 / ESU R Free: 0.162 / 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: 62.83 Å2 / Biso mean: 31.954 Å2 / Biso min: 19.73 Å2
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Refinement step | Cycle: LAST / Resolution: 1.999→108.16 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.999→2.051 Å / Total num. of bins used: 20
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