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Yorodumi- PDB-4luj: Crystal structure of Orotidine 5'-monophosphate decarboxylase fro... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4luj | ||||||
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Title | Crystal structure of Orotidine 5'-monophosphate decarboxylase from methanocaldococcus jannaschii complexed with inhibitor BMP | ||||||
Components | Orotidine 5'-phosphate decarboxylase | ||||||
Keywords | Lyase/Lyase inhibitor / tim barrel fold / OROTIDINE 5'-MONOPHOSPHATE DECARBOXYLASE / 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 | Methanocaldococcus jannaschii (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å | ||||||
Authors | Fedorov, A.A. / Fedorov, E.V. / Desai, B. / Gerlt, J.A. / Almo, S.C. | ||||||
Citation | Journal: To be Published Title: Crystal structure of Orotidine 5'-monophosphate decarboxylase from methanocaldococcus jannaschii complexed with inhibitor BMP Authors: Fedorov, A.A. / Fedorov, E.V. / Desai, B. / Gerlt, J.A. / Almo, S.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4luj.cif.gz | 186.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4luj.ent.gz | 148.8 KB | Display | PDB format |
PDBx/mmJSON format | 4luj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4luj_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 4luj_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 4luj_validation.xml.gz | 18.8 KB | Display | |
Data in CIF | 4luj_validation.cif.gz | 26.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lu/4luj ftp://data.pdbj.org/pub/pdb/validation_reports/lu/4luj | HTTPS FTP |
-Related structure data
Related structure data | 3ltpS 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
#1: Protein | Mass: 25799.191 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Methanocaldococcus jannaschii (archaea) Strain: ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440 Gene: pyrF, MJ0252 / Production host: Escherichia coli (E. coli) References: UniProt: Q57700, 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: 1.89 Å3/Da / Density % sol: 34.88 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 0.2M sodium chloride, 0.1M hepes, 20% PEG 3000, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 20, 2013 |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.075 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→33.721 Å / Num. all: 51183 / Num. obs: 51183 / % possible obs: 99.64 % / 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: 1.6→33.721 Å / SU ML: 0.17 / σ(F): 0 / Phase error: 25.22 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.6→33.721 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | S32: 0.1773 Å ° / Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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