+Open data
-Basic information
Entry | Database: PDB / ID: 3a6e | ||||||
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Title | W174F mutant creatininase, type I | ||||||
Components | Creatinine amidohydrolase | ||||||
Keywords | HYDROLASE / creatinine amidohydrolase / urease-related amidohydrolase superfamily | ||||||
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 / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Nakajima, Y. / Yamashita, K. / Ito, K. / Yoshimoto, T. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2010 Title: Substitution of Glu122 by glutamine revealed the function of the second water molecule as a proton donor in the binuclear metal enzyme creatininase Authors: Yamashita, K. / Nakajima, Y. / Matsushita, H. / Nishiya, Y. / Yamazawa, R. / Wu, Y.F. / Matsubara, F. / Oyama, H. / Ito, K. / Yoshimoto, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3a6e.cif.gz | 320.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3a6e.ent.gz | 259.1 KB | Display | PDB format |
PDBx/mmJSON format | 3a6e.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3a6e_validation.pdf.gz | 482 KB | Display | wwPDB validaton report |
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Full document | 3a6e_full_validation.pdf.gz | 498.9 KB | Display | |
Data in XML | 3a6e_validation.xml.gz | 64.3 KB | Display | |
Data in CIF | 3a6e_validation.cif.gz | 90.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a6/3a6e ftp://data.pdbj.org/pub/pdb/validation_reports/a6/3a6e | HTTPS FTP |
-Related structure data
Related structure data | 3a6dC 3a6fC 3a6gC 3a6hC 3a6jC 3a6kC 3a6lC 1j2uS S: Starting model for refinement C: citing same article (ref.) |
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Similar 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: 28559.754 Da / Num. of mol.: 6 / Mutation: W174F Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas putida (bacteria) / Plasmid: pUC19 / Production host: Escherichia coli (E. coli) / Strain (production host): XL1-Blue / References: UniProt: P83772, creatininase #2: Chemical | ChemComp-MN / #3: Chemical | ChemComp-ZN / #4: Chemical | ChemComp-CAC / #5: 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: 2.64 Å3/Da / Density % sol: 53.38 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 42%(v/v) PEG200, 10mM Magnesium chloride, 100mM Sodium cacodylate buffer, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 4r / Detector: CCD / Date: Jun 17, 2006 / Details: mirrors |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.97→50 Å / Num. all: 123961 / Num. obs: 123961 / % possible obs: 97.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Biso Wilson estimate: 20.5 Å2 / Rmerge(I) obs: 0.056 / Net I/σ(I): 34.7 |
Reflection shell | Resolution: 1.97→2.06 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.161 / Mean I/σ(I) obs: 10.6 / Num. unique all: 11025 / % possible all: 87.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1J2U Resolution: 2→20 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 23.8 Å2 | |||||||||||||||||||||||||
Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.07 Å
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