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Yorodumi- PDB-3sec: Crystal structure of Methanothermobacter thermautotrophicus oroti... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3sec | ||||||
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Title | Crystal structure of Methanothermobacter thermautotrophicus orotidine 5'-monophosphate decarboxylase complexed with pyrazofurin monophosphate | ||||||
Components | Orotidine 5'-phosphate decarboxylase | ||||||
Keywords | LYASE/LYASE INHIBITOR / orotidine 5'-monophosphate decarboxylase / Methanothermobacter thermautotrophicus / pyrazofurin monophosphate / decarboxylase / LYASE-LYASE INHIBITOR complex | ||||||
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 | Methanothermobacter thermautotrophicus (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | ||||||
Authors | Liu, Y. / Kotra, L.P. / Pai, E.F. | ||||||
Citation | Journal: To be Published Title: Crystal structure of methanococcus thermolithotrophicus orotidine 5'-monophosphate decarboxylase complexed with pyrazofurin monophosphate Authors: Liu, Y. / Kotra, L.P. / Pai, E.F. #1: Journal: Bioorg.Med.Chem. / Year: 2010 Title: Structural determinants for the inhibitory ligands of orotidine-5'-monophosphate decarboxylase. Authors: Meza-Avina, M.E. / Wei, L. / Liu, Y. / Poduch, E. / Bello, A.M. / Mishra, R.K. / 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 | 3sec.cif.gz | 62.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3sec.ent.gz | 45.5 KB | Display | PDB format |
PDBx/mmJSON format | 3sec.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/se/3sec ftp://data.pdbj.org/pub/pdb/validation_reports/se/3sec | HTTPS FTP |
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-Related structure data
Related structure data | 1dv7S 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: 26795.848 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Methanothermobacter thermautotrophicus (archaea) Strain: Delta H / Gene: 1470090, MTH_129, pyrF / Plasmid: pET15B / Production host: Escherichia coli (E. coli) References: UniProt: O26232, orotidine-5'-phosphate decarboxylase |
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#2: Chemical | ChemComp-GOL / |
#3: Chemical | ChemComp-PFU / ( |
#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: 2.08 Å3/Da / Density % sol: 40.73 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.8 Details: Trisodium Citrate, Dioxane, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 0.9002 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 7, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9002 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→50 Å / Num. obs: 24704 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 9.6 % / Rmerge(I) obs: 0.084 / Net I/σ(I): 11.7 |
Reflection shell | Resolution: 1.7→1.73 Å / Redundancy: 7.4 % / Rmerge(I) obs: 0.489 / Mean I/σ(I) obs: 4.43 / % possible all: 99.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1DV7 Resolution: 1.7→50 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.954 / SU B: 1.586 / SU ML: 0.055 / Cross valid method: THROUGHOUT / ESU R Free: 0.093 / 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: 17.911 Å2
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Refinement step | Cycle: LAST / Resolution: 1.7→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.704→1.748 Å / Total num. of bins used: 20
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