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Yorodumi- PDB-1ctu: TRANSITION-STATE SELECTIVITY FOR A SINGLE OH GROUP DURING CATALYS... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1ctu | ||||||
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Title | TRANSITION-STATE SELECTIVITY FOR A SINGLE OH GROUP DURING CATALYSIS BY CYTIDINE DEAMINASE | ||||||
Components | CYTIDINE DEAMINASE | ||||||
Keywords | HYDROLASE | ||||||
Function / homology | Function and homology information pyrimidine nucleoside binding / deoxycytidine catabolic process / cytidine deaminase / cytidine deamination / : / cytidine deaminase activity / nucleobase-containing small molecule interconversion / protein homodimerization activity / zinc ion binding / identical protein binding / cytosol Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 2.3 Å | ||||||
Authors | Xiang, S. / Short, S.A. / Wolfenden, R. / Carter, C.W. | ||||||
Citation | Journal: Biochemistry / Year: 1995 Title: Transition-state selectivity for a single hydroxyl group during catalysis by cytidine deaminase. Authors: Xiang, S. / Short, S.A. / Wolfenden, R. / Carter Jr., C.W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ctu.cif.gz | 69.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ctu.ent.gz | 51.1 KB | Display | PDB format |
PDBx/mmJSON format | 1ctu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1ctu_validation.pdf.gz | 440.7 KB | Display | wwPDB validaton report |
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Full document | 1ctu_full_validation.pdf.gz | 454 KB | Display | |
Data in XML | 1ctu_validation.xml.gz | 15 KB | Display | |
Data in CIF | 1ctu_validation.cif.gz | 20 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ct/1ctu ftp://data.pdbj.org/pub/pdb/validation_reports/ct/1ctu | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | SYMMETRY THE CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS PRESENTED BELOW GENERATE THE SUBUNITS OF THE POLYMERIC MOLECULE. APPLIED TO RESIDUES: 1 .. 616 SYMMETRY1 1 0.000000 1.000000 0.000000 0.00000 SYMMETRY2 1 1.000000 0.000000 0.000000 0.00000 SYMMETRY3 1 0.000000 0.000000 -1.000000 0.00000 |
-Components
#1: Protein | Mass: 31569.785 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / References: UniProt: P0ABF6, cytidine deaminase |
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#2: Chemical | ChemComp-ZN / |
#3: Chemical | ChemComp-ZEB / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 5.19 Å3/Da / Density % sol: 76.29 % | ||||||||||||||||||||
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Crystal | *PLUS Density % sol: 65 % | ||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / pH: 6.2 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction source | Wavelength: 1.5418 |
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Detector | Type: RIGAKU RAXIS / Detector: IMAGE PLATE |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Num. obs: 25451 / % possible obs: 80 % / Observed criterion σ(I): 1 / Redundancy: 3 % |
Reflection | *PLUS Highest resolution: 2.3 Å / Num. measured all: 72498 / Rmerge(I) obs: 0.082 |
-Processing
Software |
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Refinement | Resolution: 2.3→20 Å / σ(F): 2 /
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Displacement parameters | Biso mean: 29.4 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.25 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→20 Å
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Refine LS restraints |
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