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Yorodumi- PDB-1lp6: Crystal structure of orotidine monophosphate decarboxylase comple... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1lp6 | ||||||
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Title | Crystal structure of orotidine monophosphate decarboxylase complexed with CMP | ||||||
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 Similarity search - Function | ||||||
Biological species | Archaea (unknown) | ||||||
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 and 1001 are MET and residues 101 and 1101 are Arg ... sequence Authors state that although residues 1 and 1001 are MET and residues 101 and 1101 are Arg according to the SwissProt entry, residues 1 and 1001 were LEU and residues 101 and 1101 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 | 1lp6.cif.gz | 95.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1lp6.ent.gz | 72.7 KB | Display | PDB format |
PDBx/mmJSON format | 1lp6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lp/1lp6 ftp://data.pdbj.org/pub/pdb/validation_reports/lp/1lp6 | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | The biological unit is a dimer. |
-Components
#1: Protein | Mass: 24994.830 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Archaea (unknown) / Plasmid: pET15b / Production host: Escherichia coli (E. coli) References: UniProt: O26232, orotidine-5'-phosphate decarboxylase #2: Chemical | #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: 2.09 Å3/Da / Density % sol: 41.04 % | ||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: trisodium citrate, 1,2,3-heptanetriol, 12-crown-4, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 25K | ||||||||||||||||||||
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: Jun 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: 32661 / Num. obs: 32661 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 14.7 Å2 |
Reflection shell | Resolution: 1.9→1.97 Å / % possible all: 99.9 |
Reflection | *PLUS Lowest resolution: 30 Å / Num. measured all: 765425 / Rmerge(I) obs: 0.04 |
Reflection shell | *PLUS % possible obs: 99.9 % / Rmerge(I) obs: 0.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→28.47 Å / Rfactor Rfree error: 0.007 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 48.158 Å2 / ksol: 0.372615 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 27.9 Å2
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Refine analyze | Luzzati coordinate error free: 0.26 Å / Luzzati sigma a free: 0.18 Å | ||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→28.47 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→2.02 Å / Rfactor Rfree error: 0.018 / 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: 0.192 / Rfactor Rfree: 0.24 / Rfactor Rwork: 0.193 | ||||||||||||||||||||||||||||||||||||
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: 0.272 / Rfactor Rwork: 0.215 |