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Yorodumi- PDB-2ffc: Crystal Structure of Plasmodium Vivax Orotidine-Monophosphate-Dec... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2ffc | ||||||
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Title | Crystal Structure of Plasmodium Vivax Orotidine-Monophosphate-Decarboxyl UMP Bound | ||||||
Components | orotidine 5-monophosphate decarboxylase | ||||||
Keywords | LYASE / DECARBOXYLASE / PV-PF10_0225 / SGC / STRUCTURAL GENOMICS / STRUCTURAL GENOMICS CONSORTIUM | ||||||
Function / homology | Aldolase class I / TIM Barrel / Alpha-Beta Barrel / Alpha Beta / URIDINE-5'-MONOPHOSPHATE Function and homology information | ||||||
Biological species | Plasmodium vivax (malaria parasite P. vivax) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | ||||||
Authors | Dong, A. / Wasney, G. / Vedadi, M. / Lew, J. / Koeieradzki, I. / Zhao, Y. / Edwards, A.M. / Melone, M. / Arrowsmith, C.H. / Weigelt, J. ...Dong, A. / Wasney, G. / Vedadi, M. / Lew, J. / Koeieradzki, I. / Zhao, Y. / Edwards, A.M. / Melone, 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 999 | Sequence No suitable database references were found at time of processing |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2ffc.cif.gz | 86.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2ffc.ent.gz | 63.1 KB | Display | PDB format |
PDBx/mmJSON format | 2ffc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ff/2ffc ftp://data.pdbj.org/pub/pdb/validation_reports/ff/2ffc | HTTPS FTP |
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-Related structure data
Related structure data | 1txjC 1xccC 1y6zC 1z6gC 1z7dC 1z81C 1zo2C 2a22C 2a4aC 2aifC 2amxC 2aqwSC 2av4C 2awpC 2ayvC 2b71C 2bddC 2f4zC 2fdsC 2fo3C 2fu0C 2ghiC 2h1rC 2h2yC 2h66C 2hjrC 2hteC 2hvgC 3pggC 3tb2C 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 40191.602 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Plasmodium vivax (malaria parasite P. vivax) Plasmid: P28-LIC-THROMBIN DERIVED FROM PET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Codon plus Ril / References: EC: 4.1.3.23 |
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#2: Chemical | ChemComp-U5P / |
#3: 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: 2.1 Å3/Da / Density % sol: 41.45 % |
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Crystal grow | Temperature: 296 K / Method: vapor diffusion / pH: 8.5 Details: 30.0% PEG 4K, 0.2M NaOAc, 0.1M Tris HCl, VAPOR DIFFUSION, pH 8.5, temperature 296K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 1 Å |
Detector | Type: SBC-3 / Detector: CCD / Date: Nov 5, 2005 / Details: Si 111 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→50 Å / Num. all: 37109 / Num. obs: 37109 / % possible obs: 97.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.8 % / Biso Wilson estimate: 29.1 Å2 / Rmerge(I) obs: 0.052 / Rsym value: 0.052 / Net I/σ(I): 10.2 |
Reflection shell | Resolution: 1.7→1.72 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.612 / Mean I/σ(I) obs: 1.6 / Num. unique all: 1473 / Rsym value: 0.612 / % possible all: 80.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2AQW Resolution: 1.7→50 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.942 / SU B: 2.442 / SU ML: 0.081 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.112 / ESU R Free: 0.115 / 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: 25.437 Å2
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Refinement step | Cycle: LAST / Resolution: 1.7→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.7→1.744 Å / Total num. of bins used: 20
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