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Yorodumi- PDB-2amx: Crystal structure of Plasmodium Yoelii Adenosine deaminase (PY02076) -
+Open data
-Basic information
Entry | Database: PDB / ID: 2amx | ||||||
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Title | Crystal structure of Plasmodium Yoelii Adenosine deaminase (PY02076) | ||||||
Components | adenosine deaminase | ||||||
Keywords | HYDROLASE / Plasmodium Yoelii Adenosine deaminase (PY02076) / Structural Genomics / Structural Genomics Consortium / SGC | ||||||
Function / homology | Function and homology information deaminase activity / purine ribonucleoside monophosphate biosynthetic process Similarity search - Function | ||||||
Biological species | Plasmodium yoelii (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / SAD / Resolution: 2.02 Å | ||||||
Authors | Dong, A. / Vedadi, M. / Wasney, G. / Zhao, Y. / Lew, J. / Alam, Z. / Melone, M. / Koeieradzki, I. / Edwards, A.M. / Arrowsmith, C.H. ...Dong, A. / Vedadi, M. / Wasney, G. / Zhao, Y. / Lew, J. / Alam, Z. / Melone, M. / Koeieradzki, I. / Edwards, A.M. / Arrowsmith, C.H. / Weigelt, J. / Sundstrom, M. / Bochkarev, A. / Hui, R. / Amani, M. / Structural Genomics Consortium (SGC) | ||||||
Citation | Journal: Mol.Biochem.Parasitol. / Year: 2007 Title: Genome-scale protein expression and structural biology of Plasmodium falciparum and related Apicomplexan organisms. Authors: Vedadi, M. / Lew, J. / Artz, J. / Amani, M. / Zhao, Y. / Dong, A. / Wasney, G.A. / Gao, M. / Hills, T. / Brokx, S. / Qiu, W. / Sharma, S. / Diassiti, A. / Alam, Z. / Melone, M. / Mulichak, A. ...Authors: Vedadi, M. / Lew, J. / Artz, J. / Amani, M. / Zhao, Y. / Dong, A. / Wasney, G.A. / Gao, M. / Hills, T. / Brokx, S. / Qiu, W. / Sharma, S. / Diassiti, A. / Alam, Z. / Melone, M. / Mulichak, A. / Wernimont, A. / Bray, J. / Loppnau, P. / Plotnikova, O. / Newberry, K. / Sundararajan, E. / Houston, S. / Walker, J. / Tempel, W. / Bochkarev, A. / Kozieradzki, I. / Edwards, A. / Arrowsmith, C. / Roos, D. / Kain, K. / Hui, R. | ||||||
History |
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Remark 300 | BIOMOLECULE: 1 This entry contains the crystallographic asymmetric unit which consists of 2 chain(s) ...BIOMOLECULE: 1 This entry contains the crystallographic asymmetric unit which consists of 2 chain(s). The biological unit for the protein is not known. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2amx.cif.gz | 167.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2amx.ent.gz | 131.5 KB | Display | PDB format |
PDBx/mmJSON format | 2amx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2amx_validation.pdf.gz | 444.3 KB | Display | wwPDB validaton report |
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Full document | 2amx_full_validation.pdf.gz | 454.3 KB | Display | |
Data in XML | 2amx_validation.xml.gz | 32.7 KB | Display | |
Data in CIF | 2amx_validation.cif.gz | 48.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/am/2amx ftp://data.pdbj.org/pub/pdb/validation_reports/am/2amx | HTTPS FTP |
-Related structure data
Related structure data | 1txjC 1xccC 1y6zC 1z6gC 1z7dC 1z81C 1zo2C 2a22C 2a4aC 2aifC 2aqwC 2av4C 2awpC 2ayvC 2b71C 2bddC 2f4zC 2fdsC 2ffcC 2fo3C 2fu0C 2ghiC 2h1rC 2h2yC 2h66C 2hjrC 2hteC 2hvgC 3pggC 3tb2C C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 43336.355 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Plasmodium yoelii (eukaryote) / Plasmid: p28-LIC-Thrombin derived from pET28 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q7RMV2, adenosine deaminase #2: Chemical | ChemComp-CO / #3: Chemical | ChemComp-UNX / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
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-Sample preparation
Crystal | Density Matthews: 2.5 Å3/Da / Density % sol: 50.5 % |
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Crystal grow | Temperature: 300 K / pH: 5.5 Details: 20% PEG 3350, 0.1 M Na cacodylate pH 5.5, 0.2 M MgCl2, 10 mM CoCl2, VAPOR DIFFUSION, temperature 300 K, pH 5.50 |
-Data collection
Diffraction |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU FR-E / Wavelength: 1.5418 | |||||||||||||||
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jul 14, 2005 / Details: VERIMAX | |||||||||||||||
Radiation |
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Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 | |||||||||||||||
Reflection | Resolution: 2.02→42.9 Å / Num. all: 55108 / Num. obs: 55046 / % possible obs: 99.7 % / Observed criterion σ(I): 0 / Redundancy: 5.6 % / Rmerge(I) obs: 0.103 / Rsym value: 0.103 / Net I/σ(I): 7.2 | |||||||||||||||
Reflection shell | Resolution: 2.02→2.05 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.699 / Mean I/σ(I) obs: 2.13 / Rsym value: 0.699 / % possible all: 99.1 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.02→42.9 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.914 / SU B: 4.046 / SU ML: 0.116 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.188 / ESU R Free: 0.171 / 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: 26.6 Å2
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Refinement step | Cycle: LAST / Resolution: 2.02→42.9 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.02→2.07 Å / Total num. of bins used: 20
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