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Yorodumi- PDB-2iuo: Site Directed Mutagenesis of Key Residues Involved in the Catalyt... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2iuo | ||||||
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Title | Site Directed Mutagenesis of Key Residues Involved in the Catalytic Mechanism of Cyanase | ||||||
Components | CYANATE HYDRATASE | ||||||
Keywords | LYASE / CYANATE DEGRADATION | ||||||
Function / homology | Function and homology information cyanate catabolic process / cyanase / cyanate hydratase activity / DNA binding Similarity search - Function | ||||||
Biological species | ESCHERICHIA COLI (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Guilloton, M. / Walsh, M.A. / Joachimiak, A. / Anderson, M.P. | ||||||
Citation | Journal: To be Published 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: Journal: Structure / Year: 2000 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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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2iuo.cif.gz | 348.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2iuo.ent.gz | 285.2 KB | Display | PDB format |
PDBx/mmJSON format | 2iuo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2iuo_validation.pdf.gz | 442.2 KB | Display | wwPDB validaton report |
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Full document | 2iuo_full_validation.pdf.gz | 471.8 KB | Display | |
Data in XML | 2iuo_validation.xml.gz | 36 KB | Display | |
Data in CIF | 2iuo_validation.cif.gz | 62.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/iu/2iuo ftp://data.pdbj.org/pub/pdb/validation_reports/iu/2iuo | HTTPS FTP |
-Related structure data
Related structure data | 2iu7C 2iv1C 2ivbC 2ivgC 2ivqC 1dw9S 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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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper:
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Details | THE ENZYME IS A DECAMER MADE UO 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. |
-Components
-Protein , 1 types, 10 molecules ABCDEFGHIJ
#1: Protein | Mass: 17037.768 Da / Num. of mol.: 10 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): XL1-BLUE / References: UniProt: P00816, cyanase |
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-Non-polymers , 5 types, 2096 molecules
#2: Chemical | ChemComp-BR / #3: Chemical | ChemComp-CL / #4: Chemical | ChemComp-SO4 / #5: Chemical | ChemComp-AZI / | #6: Water | ChemComp-HOH / | |
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-Details
Sequence details | SERINE 122 MUTATED TO GLYCINE |
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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: 2.67 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: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 1.033 |
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: 1.85→40 Å / Num. obs: 129043 / % possible obs: 92.5 % / Redundancy: 2.2 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 14 |
Reflection shell | Resolution: 1.85→1.92 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.24 / Mean I/σ(I) obs: 2.5 / % possible all: 59.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1DW9 Resolution: 1.9→76.7 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.933 / SU B: 3.098 / SU ML: 0.093 / Cross valid method: THROUGHOUT / ESU R: 0.141 / ESU R Free: 0.142 / 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: 13.54 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→76.7 Å
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Refine LS restraints |
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