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Yorodumi- PDB-3mwa: Crystal structure of Plasmodium falciparum orotidine 5'-monophosp... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3mwa | ||||||
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Title | Crystal structure of Plasmodium falciparum orotidine 5'-monophosphate decarboxylase covalently modified by 2-prime-fluoro-6-iodo-UMP | ||||||
Components | Orotidine 5'-phosphate decarboxylase | ||||||
Keywords | LYASE / plasmodium falciparum / orotidine 5'-monophosphate decarboxylase / covalently / 2-prime-fluoro-6-iodo-UMP | ||||||
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 3D7 (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å | ||||||
Authors | Liu, Y. / Kotra, L.P. / Pai, E.F. | ||||||
Citation | Journal: To be Published Title: Crystal structure of Plasmodium falciparum orotidine 5'-monophosphate decarboxylase covalently modified by 2-prime-fluoro-6-iodo-UMP Authors: Liu, Y. / Kotra, L.P. / Pai, E.F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3mwa.cif.gz | 159.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3mwa.ent.gz | 123.7 KB | Display | PDB format |
PDBx/mmJSON format | 3mwa.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mw/3mwa ftp://data.pdbj.org/pub/pdb/validation_reports/mw/3mwa | HTTPS FTP |
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-Related structure data
Related structure data | 2q8lS S: Starting model for refinement |
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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 3D7 (eukaryote) / 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 #2: Chemical | #3: Chemical | ChemComp-PEG / | #4: Chemical | ChemComp-PO4 / | #5: 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: 1.89 Å3/Da / Density % sol: 34.81 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.2 Details: PEG 1000, ammonium phosphate, pH 7.2, 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 16, 2007 Details: DCM with cryo-cooled 1st crystal sagittally 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: 1.75→50 Å / Num. all: 60004 / Num. obs: 57246 / % possible obs: 97.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.6 % / Rmerge(I) obs: 0.067 / Rsym value: 0.067 / Net I/σ(I): 11 |
Reflection shell | Resolution: 1.75→1.81 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.464 / Mean I/σ(I) obs: 2.55 / Num. unique all: 5957 / Rsym value: 0.464 / % possible all: 98.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2Q8L Resolution: 1.75→50 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.953 / SU B: 2.345 / SU ML: 0.076 / Cross valid method: THROUGHOUT / ESU R Free: 0.116 / 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: 17.807 Å2
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Refinement step | Cycle: LAST / Resolution: 1.75→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.751→1.796 Å / Total num. of bins used: 20
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