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Yorodumi- PDB-1ux1: Bacillus subtilis cytidine deaminase with a Cys53His and an Arg56... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1ux1 | ||||||
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Title | Bacillus subtilis cytidine deaminase with a Cys53His and an Arg56Gln substitution | ||||||
Components | CYTIDINE DEAMINASE | ||||||
Keywords | HYDROLASE / CYTIDINE DEAMINASE / CDD / TETRAMER / ZINC BINDING / PYRIMIDINE METABOLISM / SALVAGE | ||||||
Function / homology | Function and homology information cytidine deaminase / cytidine deamination / : / cytidine deaminase activity / zinc ion binding / identical protein binding / cytosol Similarity search - Function | ||||||
Biological species | BACILLUS SUBTILIS (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.36 Å | ||||||
Authors | Johansson, E. / Neuhard, J. / Willemoes, M. / Larsen, S. | ||||||
Citation | Journal: Biochemistry / Year: 2004 Title: Structural, Kinetic, and Mutational Studies of the Zinc Ion Environment in Tetrameric Cytidine Deaminase Authors: Johansson, E. / Neuhard, J. / Willemoes, M. / Larsen, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ux1.cif.gz | 115.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ux1.ent.gz | 88.6 KB | Display | PDB format |
PDBx/mmJSON format | 1ux1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1ux1_validation.pdf.gz | 484.7 KB | Display | wwPDB validaton report |
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Full document | 1ux1_full_validation.pdf.gz | 495.8 KB | Display | |
Data in XML | 1ux1_validation.xml.gz | 23.7 KB | Display | |
Data in CIF | 1ux1_validation.cif.gz | 30.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ux/1ux1 ftp://data.pdbj.org/pub/pdb/validation_reports/ux/1ux1 | HTTPS FTP |
-Related structure data
Related structure data | 1uwzC 1ux0C 1jtkS 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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1 |
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Unit cell |
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Components on special symmetry positions |
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Noncrystallographic symmetry (NCS) | NCS oper:
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-Components
#1: Protein | Mass: 14874.952 Da / Num. of mol.: 4 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) BACILLUS SUBTILIS (bacteria) / Plasmid: PTRCC53H/R56QCDA / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): SO5201 / References: UniProt: P19079, cytidine deaminase #2: Chemical | ChemComp-THU / #3: Chemical | ChemComp-ZN / #4: Chemical | ChemComp-TRS / | #5: Water | ChemComp-HOH / | Compound details | ENGINEERED MUTATION ARG 56 GLN IN CHAINS A B C D ENGINEERED MUTATION CYS 53 HIS IN CHAINS A B C D ...ENGINEERED | |
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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: 2.1 Å3/Da / Density % sol: 41.4 % |
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Crystal grow | Method: vapor diffusion / pH: 7.5 Details: VAPOUR DIFFUSION AT RT: PROTEIN: 4.6 MG/ML, + 5 MM TETRAHYDRODEOXYURIDINE, PRECIPITANT: 30 % PEG400, 0.2M MAGNESIUM CHLORIDE, 0.1 M HEPES PH 7.5 |
-Data collection
Diffraction | Mean temperature: 120 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.542 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Sep 23, 2002 / Details: OSMIC MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.542 Å / Relative weight: 1 |
Reflection | Resolution: 2.36→25 Å / Num. obs: 21401 / % possible obs: 98.9 % / Redundancy: 6.8 % / Biso Wilson estimate: 28.3 Å2 / Rmerge(I) obs: 0.059 / Net I/σ(I): 29.8 |
Reflection shell | Resolution: 2.36→2.41 Å / Rmerge(I) obs: 0.217 / Mean I/σ(I) obs: 6.9 / % possible all: 83.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1JTK Resolution: 2.36→24.66 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 2004857.7 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 30.6894 Å2 / ksol: 0.346096 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 32.6 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.36→24.66 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.36→2.51 Å / Rfactor Rfree error: 0.022 / Total num. of bins used: 6
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Xplor file |
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