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Yorodumi- PDB-2qvn: Crystal structure of adenosine deaminase from Plasmodium vivax in... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2qvn | ||||||
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Title | Crystal structure of adenosine deaminase from Plasmodium vivax in complex with guanosine | ||||||
Components | Adenosine deaminase | ||||||
Keywords | HYDROLASE / Metallo-dependent hydrolase / TIM barrel / Structural Genomics / Medical Structural Genomics of Pathogenic Protozoa Consortium / MSGPP / Plasmodium / malaria / PSI / Protein Structure Initiative | ||||||
Function / homology | Function and homology information S-methyl-5'-thioadenosine deaminase / 5'-methylthioadenosine deaminase activity / negative regulation of adenosine receptor signaling pathway / inosine biosynthetic process / 2'-deoxyadenosine deaminase activity / adenosine deaminase / adenosine catabolic process / adenosine deaminase activity / hypoxanthine salvage / purine ribonucleoside monophosphate biosynthetic process ...S-methyl-5'-thioadenosine deaminase / 5'-methylthioadenosine deaminase activity / negative regulation of adenosine receptor signaling pathway / inosine biosynthetic process / 2'-deoxyadenosine deaminase activity / adenosine deaminase / adenosine catabolic process / adenosine deaminase activity / hypoxanthine salvage / purine ribonucleoside monophosphate biosynthetic process / purine ribonucleoside salvage / external side of plasma membrane / metal ion binding / cytosol Similarity search - Function | ||||||
Biological species | Plasmodium vivax SaI-1 (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / molecular replacement / Resolution: 2.19 Å | ||||||
Authors | Larson, E.T. / Merritt, E.A. / Structural Genomics of Pathogenic Protozoa Consortium (SGPP) | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2008 Title: Structures of substrate- and inhibitor-bound adenosine deaminase from a human malaria parasite show a dramatic conformational change and shed light on drug selectivity. Authors: Larson, E.T. / Deng, W. / Krumm, B.E. / Napuli, A. / Mueller, N. / Van Voorhis, W.C. / Buckner, F.S. / Fan, E. / Lauricella, A. / DeTitta, G. / Luft, J. / Zucker, F. / Hol, W.G. / Verlinde, C.L. / Merritt, E.A. | ||||||
History |
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Remark 999 | SEQUENCE THE SEQUENCE OF THIS PROTEIN IA ALSO AVAILABLE IN PLASMODB UNDER ACCESSION CODE PV111245. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2qvn.cif.gz | 93.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2qvn.ent.gz | 70.3 KB | Display | PDB format |
PDBx/mmJSON format | 2qvn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2qvn_validation.pdf.gz | 812.4 KB | Display | wwPDB validaton report |
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Full document | 2qvn_full_validation.pdf.gz | 814.2 KB | Display | |
Data in XML | 2qvn_validation.xml.gz | 16 KB | Display | |
Data in CIF | 2qvn_validation.cif.gz | 22.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qv/2qvn ftp://data.pdbj.org/pub/pdb/validation_reports/qv/2qvn | HTTPS FTP |
-Related structure data
Related structure data | 2pgfSC 2pgrC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | |
Other databases |
-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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-Components
#1: Protein | Mass: 43477.180 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Plasmodium vivax SaI-1 (eukaryote) / Species: Plasmodium vivax / Strain: Salvador I / Gene: Pv111245, PVX_111245 / Plasmid: BG1861 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A5KE01, adenosine deaminase |
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#2: Chemical | ChemComp-GMP / |
#3: Chemical | ChemComp-NHE / |
#4: 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: 3.08 Å3/Da / Density % sol: 60.07 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 27.3% PEG 20000, 0.1 M CHES pH 9.5, 0.1 M Sodium phosphate monobasic, 5 mM Guanosine, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.91837 Å |
Detector | Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Apr 18, 2007 / Details: mirrors |
Radiation | Monochromator: Side scattering bent cube-root I-beam single crystal; asymmetric cut 4.965 degs Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.91837 Å / Relative weight: 1 |
Reflection | Resolution: 2.19→40 Å / Num. all: 27968 / Num. obs: 27968 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.6 % / Biso Wilson estimate: 30.2 Å2 / Rmerge(I) obs: 0.146 / Χ2: 0.997 / Net I/σ(I): 5.6 |
Reflection shell | Resolution: 2.19→2.28 Å / Redundancy: 5 % / Rmerge(I) obs: 0.678 / Mean I/σ(I) obs: 1.7 / Num. unique all: 2662 / Χ2: 0.892 / % possible all: 97.1 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: PDB entry 2PGF Resolution: 2.19→35 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.917 / SU B: 10.668 / SU ML: 0.135 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.182 / ESU R Free: 0.178 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. TLS GROUPS WERE DEFINED USING THE TLSMD SERVER: J.PAINTER & E.A.MERRITT (2006) ACTA CRYST. D62, 439-450, J.PAINTER & E.A.MERRITT (2006) J. ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. TLS GROUPS WERE DEFINED USING THE TLSMD SERVER: J.PAINTER & E.A.MERRITT (2006) ACTA CRYST. D62, 439-450, J.PAINTER & E.A.MERRITT (2006) J.APPL.CRYST. 39, 109-111. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 29.408 Å2
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Refinement step | Cycle: LAST / Resolution: 2.19→35 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.19→2.245 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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