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Yorodumi- PDB-3nqg: Crystal structure of the mutant V155D of orotidine 5'-monophospha... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3nqg | |||||||||
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Title | Crystal structure of the mutant V155D of orotidine 5'-monophosphate decarboxylase from Methanobacterium thermoautotrophicum complexed with inhibitor BMP | |||||||||
Components | Orotidine 5'-phosphate decarboxylase | |||||||||
Keywords | LYASE/LYASE INHIBITOR / orotidine 5'-monophosphate decarboxylase / Methanobacterium thermoautotrophicum / inhibitor BMP / 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: 1.421 Å | |||||||||
Authors | Fedorov, A.A. / Fedorov, E.V. / Wood, B.M. / Gerlt, J.A. / Almo, S.C. | |||||||||
Citation | Journal: Biochemistry / Year: 2011 Title: Mechanism of the orotidine 5'-monophosphate decarboxylase-catalyzed reaction: importance of residues in the orotate binding site. Authors: Iiams, V. / Desai, B.J. / Fedorov, A.A. / Fedorov, E.V. / 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 | 3nqg.cif.gz | 106.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3nqg.ent.gz | 81.1 KB | Display | PDB format |
PDBx/mmJSON format | 3nqg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3nqg_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 3nqg_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 3nqg_validation.xml.gz | 22.1 KB | Display | |
Data in CIF | 3nqg_validation.cif.gz | 32.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nq/3nqg ftp://data.pdbj.org/pub/pdb/validation_reports/nq/3nqg | HTTPS FTP |
-Related structure data
Related structure data | 3nqcC 3nqdC 3nqeC 3nqfC 3nqmC 3pbuC 3pbvC 3pbwC 3pbyC 3pc0C 3g18S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 24900.654 Da / Num. of mol.: 2 / Mutation: V155D Source method: isolated from a genetically manipulated source Source: (gene. exp.) Methanothermobacter thermautotrophicus (archaea) Gene: pyrF, MTH_129 / Production host: Escherichia coli (E. coli) References: UniProt: O26232, orotidine-5'-phosphate decarboxylase #2: Chemical | #3: Chemical | ChemComp-GOL / | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.14 Å3/Da / Density % sol: 42.61 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 1.4M Sodium citrate, 0.1M hepes, pH 7.5, 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: Apr 22, 2010 |
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: 1.421→32.341 Å / Num. all: 77594 / Num. obs: 77594 / % possible obs: 97.89 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.058 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 3G18 Resolution: 1.421→32.341 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 41.843 Å2 / ksol: 0.391 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 1.421→32.341 Å
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Refine LS restraints |
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LS refinement shell |
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