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Yorodumi- PDB-3tfx: Crystal structure of Orotidine 5'-phosphate decarboxylase from La... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3tfx | ||||||
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Title | Crystal structure of Orotidine 5'-phosphate decarboxylase from Lactobacillus acidophilus | ||||||
Components | Orotidine 5'-phosphate decarboxylase | ||||||
Keywords | LYASE / PSI-Biology / NYSGRC / 000529 / Structural Genomics / New York Structural Genomics Research Consortium / TIM barrel fold / Pyrimidine metabolism / UMP biosynthesis via de novo pathway / UMP from orotate / Decarboxylase Lyase | ||||||
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 | Lactobacillus acidophilus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.19 Å | ||||||
Authors | Satyanarayana, L. / Chamala, S. / Evans, B. / Foti, R. / Gizzi, A. / Hillerich, B. / Kar, A. / LaFleur, J. / Seidel, R. / Villigas, G. ...Satyanarayana, L. / Chamala, S. / Evans, B. / Foti, R. / Gizzi, A. / Hillerich, B. / Kar, A. / LaFleur, J. / Seidel, R. / Villigas, G. / Zencheck, W. / Almo, S.C. / Swaminathan, S. / New York Structural Genomics Research Consortium (NYSGRC) | ||||||
Citation | Journal: To be Published Title: Crystal structure of Orotidine 5'-phosphate decarboxylase from Lactobacillus acidophilus Authors: Satyanarayana, L. / Almo, S.C. / Swaminathan, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3tfx.cif.gz | 100.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3tfx.ent.gz | 82.1 KB | Display | PDB format |
PDBx/mmJSON format | 3tfx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tf/3tfx ftp://data.pdbj.org/pub/pdb/validation_reports/tf/3tfx | HTTPS FTP |
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-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
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-Components
#1: Protein | Mass: 28867.941 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: Top 10 cells (Invitrogen) / Source: (gene. exp.) Lactobacillus acidophilus (bacteria) / Gene: LBA1386, pyrF, pyrF/LBA1386 / Plasmid details: T7 / Plasmid: pET3A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Codon + RIL References: UniProt: Q5FJB3, orotidine-5'-phosphate decarboxylase #2: 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: 2.36 Å3/Da / Density % sol: 47.92 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop Details: 10% w/v 1,6-Hexanediol, 0.2M MgCl2 and 20% w/v Polyethylene glycol 3350 , VAPOR DIFFUSION, SITTING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.9795 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 8, 2010 / Details: Mirrors |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 2.19→50 Å / Num. all: 27429 / Num. obs: 27429 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.1 % / Rmerge(I) obs: 0.101 / Net I/σ(I): 21.4 |
Reflection shell | Resolution: 2.19→2.27 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.122 / Num. unique all: 2716 / % possible all: 98.9 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.19→50 Å / Cor.coef. Fo:Fc: 0.922 / Cor.coef. Fo:Fc free: 0.882 / SU B: 5.45 / SU ML: 0.143 / Cross valid method: THROUGHOUT / ESU R Free: 0.214 / Stereochemistry target values: Engh & Huber / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 17.602 Å2
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Refinement step | Cycle: LAST / Resolution: 2.19→50 Å
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Refine LS restraints |
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Refine LS restraints NCS | Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 1699 / Refine-ID: X-RAY DIFFRACTION
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LS refinement shell | Resolution: 2.192→2.248 Å / Total num. of bins used: 20
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