+Open data
-Basic information
Entry | Database: PDB / ID: 1af2 | ||||||
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Title | CRYSTAL STRUCTURE OF CYTIDINE DEAMINASE COMPLEXED WITH URIDINE | ||||||
Components | CYTIDINE DEAMINASE | ||||||
Keywords | COMPLEX (HYDROLASE/PRODUCT) / DEAMINASE / PROTON TRANSFER / STRAIN / PRODUCT RELEASE / HYDROLASE / COMPLEX (HYDROLASE-PRODUCT) / COMPLEX (HYDROLASE-PRODUCT) complex | ||||||
Function / homology | Function and homology information pyrimidine nucleoside binding / deoxycytidine catabolic process / cytidine deaminase / cytidine deamination / deoxycytidine deaminase activity / 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 / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Xiang, S. / Carter, C.W. | ||||||
Citation | Journal: Biochemistry / Year: 1997 Title: The structure of the cytidine deaminase-product complex provides evidence for efficient proton transfer and ground-state destabilization. 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 | 1af2.cif.gz | 66 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1af2.ent.gz | 51.5 KB | Display | PDB format |
PDBx/mmJSON format | 1af2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/af/1af2 ftp://data.pdbj.org/pub/pdb/validation_reports/af/1af2 | HTTPS FTP |
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-Related structure data
Related structure data | 1ctuS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-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) / Production host: Escherichia coli (E. coli) / References: UniProt: P0ABF6, cytidine deaminase |
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#2: Chemical | ChemComp-ZN / |
#3: Chemical | ChemComp-U / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 5.187 Å3/Da / Density % sol: 76.289 % | |||||||||||||||||||||||||
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Crystal grow | pH: 6.2 / Details: pH 6.2 | |||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / Method: vapor diffusion, hanging drop | |||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 297 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418 |
Detector | Type: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Feb 1, 1993 / Details: MIRRORS |
Radiation | Monochromator: NI FILTER / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→20 Å / Num. obs: 24137 / % possible obs: 80 % / Observed criterion σ(I): 1 / Redundancy: 2.7 % / Rmerge(I) obs: 0.075 / Rsym value: 0.08 / Net I/σ(I): 12 |
Reflection shell | Resolution: 2.3→2.5 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.2 / Mean I/σ(I) obs: 2.5 / Rsym value: 0.22 / % possible all: 70 |
Reflection | *PLUS Num. measured all: 65003 |
Reflection shell | *PLUS % possible obs: 70 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1CTU Resolution: 2.3→7 Å / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / σ(F): 2 /
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Refinement step | Cycle: LAST / Resolution: 2.3→7 Å
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Xplor file |
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Software | *PLUS Name: X-PLOR / Version: 3 / Classification: refinement | ||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.19 | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||
Refine LS restraints | *PLUS
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