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Yorodumi- PDB-6n9m: Crystal Structure of Adenosine Deaminase from Salmonella typhimur... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6n9m | ||||||
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Title | Crystal Structure of Adenosine Deaminase from Salmonella typhimurium with Pentostatin (Deoxycoformycin) | ||||||
Components | Adenosine deaminase | ||||||
Keywords | HYDROLASE / deaminase / pentostatin / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID | ||||||
Function / homology | Function and homology information 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 | Salmonella typhimurium (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.449 Å | ||||||
Authors | Maltseva, N. / Kim, Y. / Grimshaw, S. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID) | ||||||
Citation | Journal: To Be Published 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6n9m.cif.gz | 83.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6n9m.ent.gz | 66.2 KB | Display | PDB format |
PDBx/mmJSON format | 6n9m.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/n9/6n9m ftp://data.pdbj.org/pub/pdb/validation_reports/n9/6n9m | HTTPS FTP |
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-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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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.) Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720) (bacteria) Strain: LT2 / SGSC1412 / ATCC 700720 / Gene: add, STM1463 / Plasmid: pMCSG28 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21-Gold (DE3) / References: UniProt: Q8ZPL9, adenosine deaminase |
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-Non-polymers , 5 types, 211 molecules
#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: X-RAY DIFFRACTION / Number of used crystals: 1 |
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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: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97918 Å |
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 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.449→45.937 Å / SU ML: 0.12 / Cross valid method: THROUGHOUT / σ(F): 0.31 / Phase error: 14.44
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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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