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- PDB-6n9m: Crystal Structure of Adenosine Deaminase from Salmonella typhimur... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6n9m | ||||||
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Title | Crystal Structure of Adenosine Deaminase from Salmonella typhimurium with Pentostatin (Deoxycoformycin) | ||||||
![]() | Adenosine deaminase | ||||||
![]() | HYDROLASE / deaminase / pentostatin / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID | ||||||
Function / homology | ![]() inosine biosynthetic process / adenosine deaminase / adenosine catabolic process / adenosine deaminase activity / hypoxanthine salvage / purine ribonucleoside monophosphate biosynthetic process / nucleotide metabolic process / zinc ion binding / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Maltseva, N. / Kim, Y. / Grimshaw, S. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID) | ||||||
![]() | ![]() Title: Crystal Structure of Adenosine Deaminase from Salmonella typhimurium Complexed with Pentostatin (Deoxycoformycin) (CASP target) Authors: Maltseva, N. / Kim, Y. / Grimshaw, S. / Joachimiak, A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 83.9 KB | Display | ![]() |
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PDB format | ![]() | 66.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 779.4 KB | Display | ![]() |
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Full document | ![]() | 779.5 KB | Display | |
Data in XML | ![]() | 15.2 KB | Display | |
Data in CIF | ![]() | 22.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data | |
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Other databases |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 37520.672 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: LT2 / SGSC1412 / ATCC 700720 / Gene: add, STM1463 / Plasmid: pMCSG28 / Production host: ![]() ![]() |
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-Non-polymers , 5 types, 211 molecules ![](data/chem/img/DCF.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/FMT.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/FMT.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-DCF / | ||||
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#3: Chemical | ChemComp-ZN / | ||||
#4: Chemical | #5: Chemical | ChemComp-FMT / | #6: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.9 Å3/Da / Density % sol: 35.21 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / Details: 20% PEG 3000, 0.1M Tris pH7.0, 0.2M Ca(OAc) |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Dec 17, 2017 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97918 Å / Relative weight: 1 |
Reflection | Resolution: 1.449→50 Å / Num. obs: 50915 / % possible obs: 99.3 % / Redundancy: 5.8 % / Biso Wilson estimate: 17.4 Å2 / CC1/2: 0.715 / Rsym value: 0.098 / Net I/σ(I): 23.7 |
Reflection shell | Resolution: 1.45→1.48 Å / Redundancy: 4.5 % / Mean I/σ(I) obs: 2.4 / Num. unique obs: 2471 / Rsym value: 0.683 / % possible all: 99.4 |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.449→45.937 Å
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Refine LS restraints |
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LS refinement shell |
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