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Open data
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Basic information
Entry | Database: PDB / ID: 4c5y | ||||||
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Title | Crystal structure of A. niger ochratoxinase | ||||||
![]() | OCHRATOXINASE | ||||||
![]() | HYDROLASE / METAL-DEPENDENT AMIDOHYDROLASE / OCHRATOXIN A HYDROLYSIS / AMIDOHYDROLASE SUPERFAMILY | ||||||
Function / homology | ![]() ochratoxin A catabolic process / hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds / Hydrolases; Acting on peptide bonds (peptidases); Metallocarboxypeptidases / carboxypeptidase activity / metallopeptidase activity / proteolysis / extracellular region / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Dobritzsch, D. / Wang, H. / Schneider, G. / Yu, S. | ||||||
![]() | ![]() Title: Structural and Functional Characterization of Ochratoxinase, a Novel Mycotoxin Degrading Enzyme. Authors: Dobritzsch, D. / Wang, H. / Schneider, G. / Yu, S. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 337 KB | Display | ![]() |
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PDB format | ![]() | 277.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 441.3 KB | Display | ![]() |
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Full document | ![]() | 448 KB | Display | |
Data in XML | ![]() | 31.3 KB | Display | |
Data in CIF | ![]() | 43 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4c5zC ![]() 4c60C ![]() 4c65C ![]() 2qs8S ![]() 2r8c ![]() 3be7S ![]() 3feqS ![]() 3mtwS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: ASP / Beg label comp-ID: ASP / End auth comp-ID: LEU / End label comp-ID: LEU / Refine code: _ / Auth seq-ID: 45 - 480 / Label seq-ID: 3 - 438
NCS oper: (Code: given Matrix: (0.1101, 0.9939, 0.000983), Vector: |
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Components
#1: Protein | Mass: 46689.828 Da / Num. of mol.: 2 Fragment: EXTRACELLULAR, N-TERMINALLY TRUNCATED ISOFORM, RESIDUES 43-480 Source method: isolated from a genetically manipulated source Details: 42 RESIDUES TRUNCATED AT N-TERMINUS / Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: A2R2V4, Xaa-Pro dipeptidase, Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides #2: Chemical | ChemComp-ZN / #3: Water | ChemComp-HOH / | Sequence details | THE CRYSTALLIZ | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.56 Å3/Da / Density % sol: 65.4 % / Description: NONE |
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Crystal grow | pH: 9 Details: 12% (W/V) PEG 3000, 0.1 M BICINE PH 9.0, 0.2 M TRI-POTASSIUM CITRATE |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 14, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9762 Å / Relative weight: 1 |
Reflection | Resolution: 3→72.5 Å / Num. obs: 26324 / % possible obs: 96.2 % / Observed criterion σ(I): 0 / Redundancy: 5.5 % / Rmerge(I) obs: 0.2 / Net I/σ(I): 6.3 |
Reflection shell | Resolution: 3→3.16 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.75 / Mean I/σ(I) obs: 2.2 / % possible all: 97.2 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRIES 3BE7, 3FEQ, 2R8C, 3MTW, 2QS8 Resolution: 3→67.44 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.914 / SU B: 34.251 / SU ML: 0.277 / Cross valid method: THROUGHOUT / ESU R Free: 0.359 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. DISORDERED RESIDUES A 43,A 44, B 43,B 44, B 349-351. DISORDERED REGIONS WERE NOT MODELED. RESIDUES 334-353 ADOPT DUAL CONFORMATIONS IN BOTH ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. DISORDERED RESIDUES A 43,A 44, B 43,B 44, B 349-351. DISORDERED REGIONS WERE NOT MODELED. RESIDUES 334-353 ADOPT DUAL CONFORMATIONS IN BOTH CHAINS, ONLY THE PREDOMINANT ONE WAS MODELED
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 59.349 Å2
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Refinement step | Cycle: LAST / Resolution: 3→67.44 Å
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Refine LS restraints |
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