[English] 日本語
Yorodumi- PDB-4muz: Crystal structure of orotidine 5'-monophosphate decarboxylase fro... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4muz | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of orotidine 5'-monophosphate decarboxylase from Archaeoglobus fulgidus complexed with inhibitor BMP | ||||||
Components | Orotidine 5'-phosphate decarboxylase | ||||||
Keywords | LYASE/LYASE INHIBITOR / TIM barrel / 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 Similarity search - Function | ||||||
Biological species | Archaeoglobus fulgidus (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.39 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 Archaeoglobus fulgidus complexed with inhibitor BMP Authors: Fedorov, A.A. / Fedorov, E.V. / Desai, B. / Gerlt, J.A. / Almo, S.C. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 4muz.cif.gz | 183.7 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb4muz.ent.gz | 146.4 KB | Display | PDB format |
PDBx/mmJSON format | 4muz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mu/4muz ftp://data.pdbj.org/pub/pdb/validation_reports/mu/4muz | HTTPS FTP |
---|
-Related structure data
Related structure data | 3ltpS S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 24742.773 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Archaeoglobus fulgidus (archaea) / Gene: pyrF, AF_0929 / Production host: Escherichia coli (E. coli) References: UniProt: O29333, orotidine-5'-phosphate decarboxylase #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 1.84 Å3/Da / Density % sol: 33.17 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 9.5 Details: 20% PEG 8000, 0.1M CHES, pH 9.5, VAPOR DIFFUSION, SITTING DROP, temperature 293.0K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.979 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 17, 2013 |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 1.39→40.708 Å / Num. all: 71632 / Num. obs: 71632 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3LTP Resolution: 1.39→40.708 Å / SU ML: 0.13 / σ(F): 0 / Phase error: 18.79 / Stereochemistry target values: ML
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.39→40.708 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|