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Yorodumi- PDB-1los: crystal structure of orotidine monophosphate decarboxylase mutant... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1los | ||||||
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Title | crystal structure of orotidine monophosphate decarboxylase mutant deltaR203A complexed with 6-azaUMP | ||||||
Components | orotidine monophosphate decarboxylase | ||||||
Keywords | LYASE / TIM barrel | ||||||
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 / cytosol Similarity search - Function | ||||||
Biological species | Methanothermobacter thermautotrophicus str. Delta H (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Wu, N. / Pai, E.F. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2002 Title: Crystal structures of inhibitor complexes reveal an alternate binding mode in orotidine-5'-monophosphate decarboxylase. Authors: Wu, N. / Pai, E.F. | ||||||
History |
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Remark 999 | sequence Authors state that although residues 1, 1001, 2001 and 3001 are MET and residues 101, ... sequence Authors state that although residues 1, 1001, 2001 and 3001 are MET and residues 101, 1101, 2101 and 3101 are Arg according to the SwissProt entry, residues 1, 1001, 2001 and 3001 were LEU and residues 101, 1101, 2101 and 3101 were Pro in the original construct cloned of MT genomic dna. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1los.cif.gz | 171 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1los.ent.gz | 135.5 KB | Display | PDB format |
PDBx/mmJSON format | 1los.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1los_validation.pdf.gz | 1.5 MB | Display | wwPDB validaton report |
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Full document | 1los_full_validation.pdf.gz | 1.5 MB | Display | |
Data in XML | 1los_validation.xml.gz | 34.6 KB | Display | |
Data in CIF | 1los_validation.cif.gz | 46.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lo/1los ftp://data.pdbj.org/pub/pdb/validation_reports/lo/1los | HTTPS FTP |
-Related 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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Details | The biological unit is a dimer. |
-Components
#1: Protein | Mass: 24467.234 Da / Num. of mol.: 4 / Mutation: R203A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Methanothermobacter thermautotrophicus str. Delta H (archaea) Species: Methanothermobacter thermautotrophicus / Strain: delta h / Plasmid: pET15b / Production host: Escherichia coli (E. coli) References: UniProt: O26232, orotidine-5'-phosphate decarboxylase #2: Chemical | ChemComp-UP6 / #3: 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: 2.15 Å3/Da / Density % sol: 42.73 % | ||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: trisodium citrate, MgCl2, dioxane, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K | ||||||||||||||||||
Crystal grow | *PLUS | ||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 15, 2001 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→30 Å / Num. all: 58208 / Num. obs: 58208 / % possible obs: 90.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 20.3 Å2 |
Reflection shell | Resolution: 1.9→1.97 Å / % possible all: 64 |
Reflection | *PLUS Lowest resolution: 30 Å / Num. measured all: 489020 / Rmerge(I) obs: 0.048 |
Reflection shell | *PLUS % possible obs: 64 % / Rmerge(I) obs: 0.283 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→29.39 Å / Rfactor Rfree error: 0.006 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 61.3854 Å2 / ksol: 0.388375 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 38.7 Å2
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Refine analyze | Luzzati coordinate error free: 0.28 Å / Luzzati sigma a free: 0.3 Å | ||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→29.39 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→2.02 Å / Rfactor Rfree error: 0.024 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Highest resolution: 1.9 Å / Lowest resolution: 30 Å / Rfactor all: 0.205 / Rfactor Rfree: 0.24 / Rfactor Rwork: 0.205 | ||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Highest resolution: 1.9 Å / Rfactor Rfree: 0.326 / Rfactor Rwork: 0.305 |