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Yorodumi- PDB-4lc8: Crystal structure of the mutant H128N of orotidine 5'-monophospha... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4lc8 | ||||||
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Title | Crystal structure of the mutant H128N of orotidine 5'-monophosphate decarboxylase from Methanobacterium thermoautotrophicum complexed with the inhibitor BMP | ||||||
Components | Orotidine 5'-phosphate decarboxylase | ||||||
Keywords | Lyase/Lyase Inhibitor / OMPDC fold / orotidine 5'-monophosphate decarboxylase / 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: 1.318 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 the mutant H128N of orotidine 5'-monophosphate decarboxylase from Methanobacterium thermoautotrophicum complexed with the 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 | 4lc8.cif.gz | 197.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4lc8.ent.gz | 155.7 KB | Display | PDB format |
PDBx/mmJSON format | 4lc8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4lc8_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 4lc8_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 4lc8_validation.xml.gz | 23.7 KB | Display | |
Data in CIF | 4lc8_validation.cif.gz | 35.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lc/4lc8 ftp://data.pdbj.org/pub/pdb/validation_reports/lc/4lc8 | 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
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 24860.652 Da / Num. of mol.: 2 / Mutation: H128N, R101P Source method: isolated from a genetically manipulated source Source: (gene. exp.) Methanothermobacter thermautotrophicus (archaea) Strain: ATCC 29096 / DSM 1053 / JCM 10044 / NBRC 100330 / Delta H Gene: pyrF, MTH_129 / Production host: Escherichia coli (E. coli) References: UniProt: O26232, orotidine-5'-phosphate decarboxylase |
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-Non-polymers , 5 types, 531 molecules
#2: Chemical | #3: Chemical | ChemComp-CL / #4: Chemical | #5: Chemical | ChemComp-EDO / | #6: 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: 2.14 Å3/Da / Density % sol: 42.63 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 20% PEG 8000, 0.1M Tris, 0.2M magnesium chloride, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293.0K |
-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: Jun 6, 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: 1.318→32.551 Å / Num. all: 98758 / Num. obs: 98758 / % possible obs: 99.81 % / 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: 3LTP Resolution: 1.318→32.551 Å / SU ML: 0.13 / σ(F): 0 / Phase error: 17.66 / 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: 1.318→32.551 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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