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Open data
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Basic information
Entry | Database: PDB / ID: 3a6k | ||||||
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Title | The E122Q mutant creatininase, Mn-Zn type | ||||||
![]() | Creatinine amidohydrolase | ||||||
![]() | HYDROLASE / creatinine amifohydrolase / urease-related amidohydrolase superfamily | ||||||
Function / homology | ![]() 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 | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Nakajima, Y. / Yamashita, K. / Ito, K. / Yoshimoto, T. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 309.8 KB | Display | ![]() |
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PDB format | ![]() | 253.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 476.6 KB | Display | ![]() |
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Full document | ![]() | 499.4 KB | Display | |
Data in XML | ![]() | 60.5 KB | Display | |
Data in CIF | ![]() | 83.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3a6dC ![]() 3a6eC ![]() 3a6fC ![]() 3a6gC ![]() 3a6hC ![]() 3a6jC ![]() 3a6lC ![]() 1j2tS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 28597.805 Da / Num. of mol.: 6 / Mutation: E122Q Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | ChemComp-MN / #3: Chemical | ChemComp-ZN / #4: Chemical | ChemComp-CL / #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.74 Å3/Da / Density % sol: 67.07 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 46% PEG200, 10mM Magnesium chloride, 100mM MES buffer, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 210r / Detector: CCD / Date: Nov 22, 2008 / Details: Rhodium coated silicon single crystal |
Radiation | Monochromator: Numerical link type Si(111) double crystal monochromator Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→50 Å / Num. all: 128840 / Num. obs: 128840 / % possible obs: 98.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 11.3 % / Biso Wilson estimate: 39.8 Å2 / Rmerge(I) obs: 0.118 / Net I/σ(I): 24.2 |
Reflection shell | Resolution: 2.2→2.28 Å / Redundancy: 11.3 % / Rmerge(I) obs: 0.355 / Mean I/σ(I) obs: 2.9 / Num. unique all: 12713 / % possible all: 98.8 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1J2T Resolution: 2.2→20 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber Details: The data was detwined with a twin fraction of 0.421
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Displacement parameters | Biso mean: 42.1 Å2 | |||||||||||||||||||||||||
Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.2→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.28 Å
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