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Yorodumi- PDB-3bar: Crystal structure of Plasmodium falciparum orotidine 5'-phosphate... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3bar | ||||||
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Title | Crystal structure of Plasmodium falciparum orotidine 5'-phosphate decarboxylase covalently modified by 6-azido-UMP | ||||||
Components | Orotidine 5'-phosphate decarboxylase | ||||||
Keywords | LYASE / Plasmodium falciparum / orotidine 5'-phosphate decarboxylase / covalently / 6-azido-UMP / Pyrimidine biosynthesis | ||||||
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: 1.9 Å | ||||||
Authors | Liu, Y. / Bello, A.M. / Poduch, E. / Lau, W. / Kotra, L.P. / Pai, E.F. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2008 Title: Structure-Activity Relationships of C6-Uridine Derivatives Targeting Plasmodia Orotidine Monophosphate Decarboxylase. Authors: Bello, A.M. / Poduch, E. / Liu, Y. / Wei, L. / Crandall, I. / Wang, X. / Dyanand, C. / Kain, K.C. / Pai, E.F. / Kotra, L.P. | ||||||
History |
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Remark 600 | HETEROGEN THERE IS A COVALENT BOND FORMED BETWEEN CARBON-6 OF THE URIDINE RING OF UMP AND THE NZ- ... HETEROGEN THERE IS A COVALENT BOND FORMED BETWEEN CARBON-6 OF THE URIDINE RING OF UMP AND THE NZ-NITROGEN OF LYS138 |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3bar.cif.gz | 149.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3bar.ent.gz | 116.5 KB | Display | PDB format |
PDBx/mmJSON format | 3bar.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3bar_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 3bar_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 3bar_validation.xml.gz | 28 KB | Display | |
Data in CIF | 3bar_validation.cif.gz | 39.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ba/3bar ftp://data.pdbj.org/pub/pdb/validation_reports/ba/3bar | HTTPS FTP |
-Related structure data
Related structure data | 2q8zC 2qafC 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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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 39899.457 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum) Strain: 3D7 / Gene: ompdc / Plasmid: pET28a-LIC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-RIL(DE23) References: UniProt: Q8T6J6, UniProt: Q8IJH3*PLUS, orotidine-5'-phosphate decarboxylase #2: Chemical | #3: Water | ChemComp-HOH / | Nonpolymer details | THERE IS A COVALENT BOND FORMED BETWEEN CARBON-6 OF THE URIDINE RING OF UMP AND THE NZ-NITROGEN OF LYS138 | |
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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: 1.9 Å3/Da / Density % sol: 35.24 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9.2 Details: 100mM Ammonium phosphate, 27% PEG 1000, pH 9.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97934 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Aug 15, 2007 Details: DCM with cryo-cooled 1st crystal sagitally bent 2nd crystal followed by vertically focusing mirror |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97934 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→50 Å / Num. all: 44155 / Num. obs: 44155 / % possible obs: 95.37 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.2 % / Rmerge(I) obs: 0.085 / Rsym value: 0.085 / Net I/σ(I): 11.4 |
Reflection shell | Resolution: 1.9→1.97 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.459 / Mean I/σ(I) obs: 3.45 / Num. unique all: 4703 / Rsym value: 0.459 / % possible all: 97.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 2Q8L Resolution: 1.9→24.68 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.938 / SU B: 3.192 / SU ML: 0.097 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.173 / ESU R Free: 0.154 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: Program coot 0.1.3-pre-1 has also been used in refinement
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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: 22.075 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→24.68 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→1.95 Å / Total num. of bins used: 20
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