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- PDB-2ivb: 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: 2ivb | ||||||
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Title | SITE DIRECTED MUTAGENESIS OF KEY RESIDUES INVOLVED IN THE CATALYTIC MECHANISM OF CYANASE | ||||||
![]() | CYANATE HYDRATASE | ||||||
![]() | LYASE / MIDWEST CENTER FOR STRUCTURAL GENOMICS / PROTEIN STRUCTURE INITIATIVE / PSI / MCSG / CYANATE DEGRADATION | ||||||
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 Formation of the Enzyme Active Site. Authors: Walsh, M.A. / Otwinowski, Z. / Perrakis, A. / Anderson, P.M. / Joachimiak, A. | ||||||
History |
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Remark 700 | SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED. |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 366.5 KB | Display | ![]() |
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PDB format | ![]() | 300.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 2iu7C ![]() 2iuoC ![]() 2iv1C ![]() 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 ENZYME IS A DECAMER MADE UP OF 5 DIMERS. 4 SUBUNITSCONTRIBUTE TO MAKING UP THE 5 ACTIVE SITES OF THISDECAMERIC ENZYME.THE DECAMER COULD BE VISUALIZED AS JI/CH/GE/FB/DA DIMERS. |
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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-SO4 / #3: Chemical | ChemComp-CL / #4: Chemical | ChemComp-AZI / #5: 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 | SERINE 122 MUTATED TO ALANINE | |
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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 % / Description: NONE |
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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: ADSC CCD / Detector: CCD / Details: MIRRORS |
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: 1.95→75 Å / Num. obs: 115164 / % possible obs: 95.7 % / Redundancy: 2 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 17.3 |
Reflection shell | Resolution: 1.95→2.05 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.2 / Mean I/σ(I) obs: 5.3 / % possible all: 84.6 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1DW9 Resolution: 1.95→75.38 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.933 / SU B: 3.365 / SU ML: 0.1 / Cross valid method: THROUGHOUT / ESU R: 0.16 / ESU R Free: 0.154 / 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: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 17.63 Å2
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Refinement step | Cycle: LAST / Resolution: 1.95→75.38 Å
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Refine LS restraints |
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