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Yorodumi- PDB-2q58: Cryptosporidium parvum putative polyprenyl pyrophosphate synthase... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2q58 | |||||||||
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Title | Cryptosporidium parvum putative polyprenyl pyrophosphate synthase (cgd4_2550) in complex with zoledronate | |||||||||
Components | Farnesyl pyrophosphate synthase | |||||||||
Keywords | TRANSFERASE / FARNESYL DIPHOSPHATE SYNTHASE / STRUCTURAL GENOMICS / STRUCTURAL GENOMICS CONSORTIUM / SGC | |||||||||
Function / homology | Function and homology information farnesyl diphosphate biosynthetic process / dimethylallyltranstransferase activity / geranyltranstransferase activity / metal ion binding / cytoplasm Similarity search - Function | |||||||||
Biological species | Cryptosporidium parvum (eukaryote) | |||||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.37 Å | |||||||||
Authors | Chruszcz, M. / Artz, J. / Zheng, H. / Dong, A. / Dunford, J. / Lew, J. / Zhao, Y. / Kozieradski, I. / Kavanaugh, K.L. / Opperman, U. ...Chruszcz, M. / Artz, J. / Zheng, H. / Dong, A. / Dunford, J. / Lew, J. / Zhao, Y. / Kozieradski, I. / Kavanaugh, K.L. / Opperman, U. / Sundstrom, M. / Weigelt, J. / Edwards, A. / Arrowsmith, C. / Bochkarev, A. / Hui, R. / Minor, W. / Structural Genomics Consortium (SGC) | |||||||||
Citation | Journal: Chem.Biol. / Year: 2008 Title: Targeting a uniquely nonspecific prenyl synthase with bisphosphonates to combat cryptosporidiosis Authors: Artz, J.D. / Dunford, J.E. / Arrowood, M.J. / Dong, A. / Chruszcz, M. / Kavanagh, K.L. / Minor, W. / Russell, R.G. / Ebetino, F.H. / Oppermann, U. / Hui, R. #1: 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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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2q58.cif.gz | 151 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2q58.ent.gz | 116.1 KB | Display | PDB format |
PDBx/mmJSON format | 2q58.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/q5/2q58 ftp://data.pdbj.org/pub/pdb/validation_reports/q5/2q58 | HTTPS FTP |
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-Related structure data
Related structure data | 2o1oC 1yv5S S: Starting model for refinement 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: 42973.051 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Cryptosporidium parvum (eukaryote) / Strain: Iowa II / Gene: CGD4_2550 / Plasmid: P28A-LIC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-(DE3)-CONDOMPLUS-RIL / References: UniProt: Q5CR09 #2: Chemical | ChemComp-MG / #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.62 Å3/Da / Density % sol: 53.03 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / pH: 7.5 Details: 1.6M AMMONIUM SULFATE, 10MM MAGNESIUM CHLORIDE, 100MM HEPES, PH 7.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K, PH 7.50 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54178 / Wavelength: 1.54178 Å |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: May 5, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54178 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→50 Å / Num. all: 44405 / Num. obs: 44405 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 5.6 % / Rmerge(I) obs: 0.038 / Rsym value: 0.038 / Net I/σ(I): 34.1 |
Reflection shell | Resolution: 2.2→2.28 Å / Redundancy: 5.3 % / Mean I/σ(I) obs: 1.7 / % possible all: 98.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1YV5 Resolution: 2.37→30.46 Å / Num. parameters: 21544 / Num. restraintsaints: 22140 / Cross valid method: FREE R / σ(F): 0 / σ(I): 0 / Stereochemistry target values: ENGH AND HUBER
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Refine analyze | Num. disordered residues: 0 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 5385 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.37→30.46 Å
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Refine LS restraints |
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