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Open data
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Basic information
Entry | Database: PDB / ID: 5xkp | ||||||
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Title | Crystal structure of Msmeg3575 in complex with 5-azacytosine | ||||||
![]() | CMP/dCMP deaminase, zinc-binding protein | ||||||
![]() | HYDROLASE / deaminase / CDA fold / 5-azacytosine | ||||||
Function / homology | ![]() cytidine metabolic process / pyrimidine-containing compound salvage / cytosine deaminase activity / cytosine metabolic process / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Gaded, V.M. / Anand, R. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Selective Deamination of Mutagens by a Mycobacterial Enzyme Authors: Gaded, V. / Anand, R. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 132.4 KB | Display | ![]() |
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PDB format | ![]() | 101.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 480.8 KB | Display | ![]() |
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Full document | ![]() | 485.1 KB | Display | |
Data in XML | ![]() | 24.3 KB | Display | |
Data in CIF | ![]() | 32.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5xkoSC ![]() 5xkqC ![]() 5xkrC 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 domain:
NCS domain segments: Component-ID: _ / Beg auth comp-ID: ALA / Beg label comp-ID: ALA / End auth comp-ID: ARG / End label comp-ID: ARG / Refine code: _ / Auth seq-ID: 2 - 159 / Label seq-ID: 1 - 158
NCS ensembles :
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Components
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 17132.191 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Details: 5-azacytosine is used as a chemotherapeutic drug Source: (gene. exp.) ![]() Strain: ATCC 700084 / mc(2)155 / Gene: MSMEG_3575, MSMEI_3493 / Plasmid: pET28a / Cell line (production host): BL21 DE3 / Production host: ![]() ![]() |
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-Non-polymers , 5 types, 45 molecules ![](data/chem/img/5AZ.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-5AZ / #3: Chemical | ChemComp-ZN / #4: Chemical | ChemComp-GOL / #5: Chemical | ChemComp-ACT / | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.48 Å3/Da / Density % sol: 50.52 % / Description: Flat plate like crystals |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop Details: 0.2 M magnesium acetate tetrahydrate, 0.1 M Tris-HCl (pH 6.4) and 20% PEG 8000 PH range: 6.0 - 7.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 2, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 3→62.08 Å / Num. obs: 13940 / % possible obs: 99.1 % / Redundancy: 5 % / Rsym value: 0.106 / Net I/σ(I): 10.6 |
Reflection shell | Resolution: 3→3.1 Å |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5XKO Resolution: 3→62.08 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.889 / SU B: 19.998 / SU ML: 0.344 / Cross valid method: THROUGHOUT / ESU R Free: 0.457 / 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: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 58.792 Å2
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Refinement step | Cycle: 1 / Resolution: 3→62.08 Å
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Refine LS restraints |
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