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Open data
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Basic information
Entry | Database: PDB / ID: 5xkr | ||||||
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Title | Crystal structure of Msmeg3575 in complex with benzoguanamine | ||||||
![]() | CMP/dCMP deaminase, zinc-binding protein | ||||||
![]() | HYDROLASE / cda fold / deaminase / benzoguanamine | ||||||
Function / homology | ![]() cytidine metabolic process / pyrimidine-containing compound salvage / cytosine deaminase activity / cytosine metabolic process / metal ion binding 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 | ![]() | 171.6 KB | Display | ![]() |
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PDB format | ![]() | 133.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 496 KB | Display | ![]() |
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Full document | ![]() | 507.6 KB | Display | |
Data in XML | ![]() | 42.3 KB | Display | |
Data in CIF | ![]() | 65.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5xkoSC ![]() 5xkpC ![]() 5xkqC 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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2 | ![]()
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Unit cell |
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Components
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 17263.387 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source 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, 1285 molecules ![](data/chem/img/BZE.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-BZE / #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: 2.55 Å3/Da / Density % sol: 51.89 % / Description: Flat plate like crystals |
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, hanging drop Details: 0.2 M magnesium acetate tetrahydrate, 0.1 M Tris HCl pH 6.2 and 15% 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 3, 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: 1.38→108.57 Å / Num. obs: 145157 / % possible obs: 98.3 % / Redundancy: 3.9 % / Rsym value: 0.045 / Net I/σ(I): 25.7 |
Reflection shell | Resolution: 1.38→1.45 Å |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5XKO Resolution: 1.38→108.57 Å / Cor.coef. Fo:Fc: 0.982 / Cor.coef. Fo:Fc free: 0.974 / SU B: 0.689 / SU ML: 0.028 / Cross valid method: THROUGHOUT / ESU R: 0.043 / ESU R Free: 0.047 / 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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 18.148 Å2
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Refinement step | Cycle: 1 / Resolution: 1.38→108.57 Å
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Refine LS restraints |
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