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- PDB-2iu7: Site directed mutagenesis of key residues involved in the catalyt... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2iu7 | ||||||
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Title | Site directed mutagenesis of key residues involved in the catalytic mechanism of Cyanase | ||||||
![]() | CYANATE HYDRATASE | ||||||
![]() | LYASE | ||||||
Function / homology | ![]() cyanate catabolic process / cyanase / cyanate hydratase activity / DNA binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Guilloton, M. / Walsh, M.A. / Joachimiak, A. / Anderson, P.M. | ||||||
![]() | ![]() Title: A Twin Set of Low Pka Arginines Ensures the Concerted Acid Base Catalytic Mechanism of Cyanase Authors: Guilloton, M. / Walsh, M.A. / Joachimiak, A. / Anderson, P.M. #1: ![]() Title: Structure of Cyanase Reveals that a Novel Dimeric and Decameric Arrangement of Subunits is Required for the Formation of the Enzyme Active Site Authors: Walsh, M.A. / Otwinowski, Z. / Perrakis, A. / Anderson, P.M. / Joachimiak, A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 374.9 KB | Display | ![]() |
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PDB format | ![]() | 307.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 452.2 KB | Display | ![]() |
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Full document | ![]() | 479.5 KB | Display | |
Data in XML | ![]() | 35.7 KB | Display | |
Data in CIF | ![]() | 67.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2iuoC ![]() 2iv1C ![]() 2ivbC ![]() 2ivgC ![]() 2ivqC ![]() 1dw9S 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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Noncrystallographic symmetry (NCS) | NCS oper:
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Details | THE CYANASE DECAMER IS A PENTAMER OF DIMERS. THE FIVEDIMERS ARE MADE UP FROM THE FOLLOWING CHAIN IDENTIFIERS:A:D, B:F, C:H, G: H AND I:J. TWO SETS OF DIMERS CONTRIBUTETO THE MAKE UP OF THE 5 ACTIVE SITES OF THE ENZYME . INTHIS STRUCTURE OXALATE IS BOUND TO EACH ACTIVE SITEDESIGNATED AS AC1 (DIMERS A:D, B:F ), AC2 (DIMERS A:D,I:J)AC3,(DIMERS I:J AC4 , AC5 (SEE REMARK 800). |
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Components
#1: Protein | Mass: 17051.793 Da / Num. of mol.: 10 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | ChemComp-OXL / #3: Chemical | ChemComp-SO4 / #4: Water | ChemComp-HOH / | Compound details | CATALYZES THE REACTION OF CYANATE WITH BICARBONATE TO PRODUCE AMMONIA AND CARBON DIOXIDE. ...CATALYZES THE REACTION OF CYANATE WITH BICARBONAT | Sequence details | TYROSINE 95 MUTATED TO PHENYLALAN | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.67 Å3/Da / Density % sol: 54 % |
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Crystal grow | Method: vapor diffusion, sitting drop / pH: 7.3 Details: CRYSTALS WERE GROWN BY THE SITTING DROP METHOD OF VAPOUR DIFFUSION FROM 50% AMMONIUM SULPHATE SOLUTIONS BUFFERED WITH 50MM NAKPO4, PH = 7.3, AND IN THE PRESENCE OF 50 MM TRIC/HCL, PH =7.3. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: CUSTOM / Detector: CCD / Details: MIRROR |
Radiation | Monochromator: SI 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.033 Å / Relative weight: 1 |
Reflection | Resolution: 1.91→99 Å / Num. obs: 1 / % possible obs: 96.8 % / Redundancy: 2.1 % / Rmerge(I) obs: 0.03 / Net I/σ(I): 25.4 |
Reflection shell | Resolution: 1.91→1.98 Å / Redundancy: 1.6 % / Rmerge(I) obs: 0.1 / Mean I/σ(I) obs: 7.3 / % possible all: 91.2 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1DW9 Resolution: 1.91→76.25 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.943 / SU B: 2.577 / SU ML: 0.077 / Cross valid method: THROUGHOUT / ESU R: 0.123 / ESU R Free: 0.126 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
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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: 20.72 Å2
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Refinement step | Cycle: LAST / Resolution: 1.91→76.25 Å
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Refine LS restraints |
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