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Yorodumi- PDB-3mo7: Crystal structure of human orotidine 5'-monophosphate decarboxyla... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3mo7 | ||||||
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Title | Crystal structure of human orotidine 5'-monophosphate decarboxylase covalently modified by 2'-fluoro-6-iodo-UMP | ||||||
Components | Uridine 5'-monophosphate synthase | ||||||
Keywords | LYASE / UMP synthase / Orotidine 5'-monophosphate Decarboxylase / 2'-fluoro-6-iodo-UMP | ||||||
Function / homology | Function and homology information UMP biosynthetic process / orotate phosphoribosyltransferase / orotate phosphoribosyltransferase activity / pyrimidine nucleobase biosynthetic process / Pyrimidine biosynthesis / UDP biosynthetic process / orotidine-5'-phosphate decarboxylase / orotidine-5'-phosphate decarboxylase activity / 'de novo' UMP biosynthetic process / 'de novo' pyrimidine nucleobase biosynthetic process ...UMP biosynthetic process / orotate phosphoribosyltransferase / orotate phosphoribosyltransferase activity / pyrimidine nucleobase biosynthetic process / Pyrimidine biosynthesis / UDP biosynthetic process / orotidine-5'-phosphate decarboxylase / orotidine-5'-phosphate decarboxylase activity / 'de novo' UMP biosynthetic process / 'de novo' pyrimidine nucleobase biosynthetic process / lactation / female pregnancy / cellular response to xenobiotic stimulus / identical protein binding / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 Å | ||||||
Authors | Liu, Y. / Kotra, L.P. / Pai, E.F. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2011 Title: Novel interactions of fluorinated nucleotide derivatives targeting orotidine 5'-monophosphate decarboxylase. Authors: Lewis, M. / Meza-Avina, M.E. / Wei, L. / Crandall, I.E. / Bello, A.M. / Poduch, E. / Liu, Y. / Paige, C.J. / Kain, K.C. / Pai, E.F. / 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 | 3mo7.cif.gz | 77.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3mo7.ent.gz | 56.3 KB | Display | PDB format |
PDBx/mmJSON format | 3mo7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mo/3mo7 ftp://data.pdbj.org/pub/pdb/validation_reports/mo/3mo7 | HTTPS FTP |
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-Related structure data
Related structure data | 2p1fS 3bko 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: 30472.162 Da / Num. of mol.: 1 Fragment: Orotidine 5'-phosphate decarboxylase domain residues 223-480 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: gi|13960142, OK/SW-cl.21, UMPS / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS References: UniProt: P11172, orotidine-5'-phosphate decarboxylase |
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#2: Chemical | ChemComp-UFT / |
#3: Chemical | ChemComp-GOL / |
#4: 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: 2.32 Å3/Da / Density % sol: 46.99 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: Sodium Citrate, pH 7.5, 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: 1.35→50 Å / Num. all: 58884 / Num. obs: 56107 / % possible obs: 94.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.8 % / Rmerge(I) obs: 0.073 / Rsym value: 0.073 / Net I/σ(I): 11.2 |
Reflection shell | Resolution: 1.35→1.4 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.476 / Mean I/σ(I) obs: 3.1 / Num. unique all: 6052 / Rsym value: 0.476 / % possible all: 97.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 2P1F Resolution: 1.35→23.61 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.966 / SU B: 0.753 / SU ML: 0.031 / Cross valid method: THROUGHOUT / ESU R: 0.052 / ESU R Free: 0.053 / 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: 13.982 Å2
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Refinement step | Cycle: LAST / Resolution: 1.35→23.61 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.349→1.384 Å / Total num. of bins used: 20
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