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Yorodumi- PDB-3s9y: Crystal Structure of P. falciparum orotidine 5'-monophosphate dec... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3s9y | ||||||
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Title | Crystal Structure of P. falciparum orotidine 5'-monophosphate decarboxylase complexed with 5-fluoro-6-amino-UMP in space group P21, produced from 5-fluoro-6-azido-UMP | ||||||
Components | Orotidine 5'-phosphate decarboxylase | ||||||
Keywords | LYASE / P. falciparum / orotidine 5'-monophosphate decarboxylase / 5-fluoro-6-amino-UMP / 5-fluoro-6-azido-UMP / decarboxylase | ||||||
Function / homology | Function and homology information orotidine-5'-phosphate decarboxylase / orotidine-5'-phosphate decarboxylase activity / 'de novo' UMP biosynthetic process / 'de novo' pyrimidine nucleobase biosynthetic process Similarity search - Function | ||||||
Biological species | Plasmodium falciparum (malaria parasite P. falciparum) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | ||||||
Authors | Liu, Y. / Kotra, L.P. / Pai, E.F. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2009 Title: Structure-activity relationships of orotidine-5'-monophosphate decarboxylase inhibitors as anticancer agents. Authors: Bello, A.M. / Konforte, D. / Poduch, E. / Furlonger, C. / Wei, L. / Liu, Y. / Lewis, M. / Pai, E.F. / Paige, C.J. / Kotra, L.P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3s9y.cif.gz | 309.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3s9y.ent.gz | 248.4 KB | Display | PDB format |
PDBx/mmJSON format | 3s9y.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/s9/3s9y ftp://data.pdbj.org/pub/pdb/validation_reports/s9/3s9y | HTTPS FTP |
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-Related structure data
Related structure data | 3g3dC 3g3mC 2q8lS 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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2 |
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Unit cell |
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-Components
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 39899.457 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum) Strain: 3D7 / Gene: gi|9310996, PF10_0225 / Plasmid: pET28a-LIC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-RIL(DE23) References: UniProt: Q8IJH3, orotidine-5'-phosphate decarboxylase |
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-Non-polymers , 6 types, 1140 molecules
#2: Chemical | ChemComp-FNU / #3: Chemical | ChemComp-SO4 / | #4: Chemical | ChemComp-PGE / | #5: Chemical | ChemComp-PEG / | #6: Chemical | #7: 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: 2.04 Å3/Da / Density % sol: 39.67 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.6 Details: PEG1000, pH 8.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 0.9002 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 22, 2007 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9002 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→50 Å / Num. all: 139725 / Num. obs: 135063 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.1 % / Rmerge(I) obs: 0.066 / Rsym value: 0.066 / Net I/σ(I): 9.2 |
Reflection shell | Resolution: 1.7→1.73 Å / Redundancy: 4 % / Rmerge(I) obs: 0.487 / Mean I/σ(I) obs: 2.69 / Num. unique all: 6930 / % possible all: 98.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: pdb entry 2Q8L Resolution: 1.7→25.99 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.946 / SU B: 2.019 / SU ML: 0.068 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.107 / 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: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 18.24 Å2
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Refinement step | Cycle: LAST / Resolution: 1.7→25.99 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.701→1.745 Å / Total num. of bins used: 20
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