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Yorodumi- PDB-3g1d: Crystal structure of orotidine 5'-monophosphate decarboxylase fro... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3g1d | ||||||
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Title | Crystal structure of orotidine 5'-monophosphate decarboxylase from Methanobacterium thermoautotrophicum complexed with uridine 5'-monophosphate | ||||||
Components | Orotidine 5'-phosphate decarboxylase | ||||||
Keywords | LYASE / orotidine 5'-monophosphate decarboxylase / UMP / Decarboxylase / Pyrimidine biosynthesis | ||||||
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 str. Delta H (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å | ||||||
Authors | Fedorov, A.A. / Fedorov, E.V. / Chan, K.K. / Gerlt, J.A. / Almo, S.C. | ||||||
Citation | Journal: Biochemistry / Year: 2009 Title: Mechanism of the orotidine 5'-monophosphate decarboxylase-catalyzed reaction: evidence for substrate destabilization. Authors: Chan, K.K. / Wood, B.M. / Fedorov, A.A. / Fedorov, E.V. / Imker, H.J. / Amyes, T.L. / Richard, J.P. / Almo, S.C. / Gerlt, J.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3g1d.cif.gz | 99.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3g1d.ent.gz | 74.8 KB | Display | PDB format |
PDBx/mmJSON format | 3g1d.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/g1/3g1d ftp://data.pdbj.org/pub/pdb/validation_reports/g1/3g1d | HTTPS FTP |
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-Related structure data
Related structure data | 3g18SC 3g1aC 3g1fC 3g1hC 3g1sC 3g1vC 3g1xC 3g1yC 3g22C 3g24C 3gdkC 3gdlC 3gdrC 3gdtC S: Starting model for refinement C: citing same article (ref.) |
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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
#1: Protein | Mass: 24884.697 Da / Num. of mol.: 2 / Mutation: R101P Source method: isolated from a genetically manipulated source Source: (gene. exp.) Methanothermobacter thermautotrophicus str. Delta H (archaea) Gene: pyrF, MTH_129 / 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 |
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-Sample preparation
Crystal | Density Matthews: 2.15 Å3/Da / Density % sol: 42.69 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: 30% 4000, 0.1M sodium citrate, 0.2M ammonium acetate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.97915 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 19, 2007 |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97915 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→25 Å / Num. all: 65391 / Num. obs: 65391 / % possible obs: 97 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.071 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3G18 Resolution: 1.5→25 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 1.5→25 Å
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Refine LS restraints |
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