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Yorodumi- PDB-3sj3: Crystal structure of the mutant R160A.Y206F of orotidine 5'-monop... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3sj3 | ||||||
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Title | Crystal structure of the mutant R160A.Y206F of orotidine 5'-monophosphate decarboxylase from Methanobacterium thermoautotrophicum complexed with the inhibitor BMP | ||||||
Components | Orotidine 5'-phosphate decarboxylase | ||||||
Keywords | lyase/lyase inhibitor / tim barrel / 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 / cytosol Similarity search - Function | ||||||
Biological species | Methanothermobacter thermautotrophicus (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.26 Å | ||||||
Authors | Fedorov, A.A. / Fedorov, E.V. / Desai, B. / Gerlt, J.A. / Almo, S.C. | ||||||
Citation | Journal: Biochemistry / Year: 2012 Title: Conformational changes in orotidine 5'-monophosphate decarboxylase: a structure-based explanation for how the 5'-phosphate group activates the enzyme. Authors: Desai, B.J. / Wood, B.M. / Fedorov, A.A. / Fedorov, E.V. / Goryanova, B. / 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 | 3sj3.cif.gz | 110.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3sj3.ent.gz | 84.2 KB | Display | PDB format |
PDBx/mmJSON format | 3sj3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sj/3sj3 ftp://data.pdbj.org/pub/pdb/validation_reports/sj/3sj3 | HTTPS FTP |
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-Related structure data
Related structure data | 3li0C 3p5yC 3p5zC 3p60C 3p61C 3qezC 3qf0C 3qmrC 3qmsC 3qmtC 3rluC 3rlvC 3v1pC 4fx6C 4fx8C 4fxrC 4gc4C 3ltpS 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: 24782.582 Da / Num. of mol.: 2 / Mutation: R160A, Y206F Source method: isolated from a genetically manipulated source Source: (gene. exp.) Methanothermobacter thermautotrophicus (archaea) Strain: Delta H / 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 / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.16 Å3/Da / Density % sol: 43.1 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 30% PEG 4000, 0.1M Tris.HCl. 0.2M magnesium chloride, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K |
-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: Jun 8, 2011 |
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: 1.26→32.527 Å / Num. all: 111994 / Num. obs: 111994 / % possible obs: 98.38 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 3LTP Resolution: 1.26→32.527 Å / SU ML: 0.18 / σ(F): 0 / Phase error: 18.35 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.38 Å / VDW probe radii: 0.7 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 54.443 Å2 / ksol: 0.415 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 1.26→32.527 Å
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Refine LS restraints |
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LS refinement shell |
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