+Open data
-Basic information
Entry | Database: PDB / ID: 1q3k | ||||||
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Title | Crystal structure of creatinine amidohydrolase (creatininase) | ||||||
Components | creatininase | ||||||
Keywords | HYDROLASE / alpha-beta-fold | ||||||
Function / homology | Function and homology information creatininase / creatininase activity / creatinine catabolic process / creatine biosynthetic process / hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides / riboflavin biosynthetic process / manganese ion binding / zinc ion binding Similarity search - Function | ||||||
Biological species | Pseudomonas putida (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.1 Å | ||||||
Authors | Beuth, B. / Niefind, K. / Schomburg, D. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2003 Title: Crystal structure of creatininase from Pseudomonas putida: A novel fold and a case of convergent evolution Authors: Beuth, B. / Niefind, K. / Schomburg, D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1q3k.cif.gz | 318.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1q3k.ent.gz | 258.8 KB | Display | PDB format |
PDBx/mmJSON format | 1q3k.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1q3k_validation.pdf.gz | 485.4 KB | Display | wwPDB validaton report |
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Full document | 1q3k_full_validation.pdf.gz | 533.5 KB | Display | |
Data in XML | 1q3k_validation.xml.gz | 68 KB | Display | |
Data in CIF | 1q3k_validation.cif.gz | 93.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/q3/1q3k ftp://data.pdbj.org/pub/pdb/validation_reports/q3/1q3k | 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: 28428.539 Da / Num. of mol.: 6 / Fragment: enzyme Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas putida (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: P83772, creatininase #2: Chemical | ChemComp-ZN / #3: Chemical | ChemComp-GOL / #4: 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: 2.18 Å3/Da / Density % sol: 43 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: PEG 8000, ethanol, HEPES, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K | ||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 293 K / pH: 8 / Method: vapor diffusion, sitting drop | ||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 0.8428 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Aug 24, 2000 |
Radiation | Monochromator: triangular monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8428 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→50 Å / Num. all: 90353 / Num. obs: 71469 / % possible obs: 79.1 % / Observed criterion σ(I): -3 / Redundancy: 3.1 % / Biso Wilson estimate: 31.5 Å2 / Rsym value: 0.039 / Net I/σ(I): 22.5 |
Reflection shell | Resolution: 2.1→2.18 Å / Mean I/σ(I) obs: 1.8 / Rsym value: 0.309 / % possible all: 52.5 |
Reflection | *PLUS Highest resolution: 2.1 Å / Lowest resolution: 30 Å / Num. measured all: 223797 / Rmerge(I) obs: 0.039 |
Reflection shell | *PLUS % possible obs: 52.5 % / Rmerge(I) obs: 0.309 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2.1→50 Å / Isotropic thermal model: isotropic / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 38 Å2 | |||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.31 Å | |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.1→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.15 Å
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Refinement | *PLUS Highest resolution: 2.1 Å / Lowest resolution: 30 Å | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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