+Open data
-Basic information
Entry | Database: PDB / ID: 2vjp | ||||||
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Title | Formyl-CoA transferase mutant variant W48F | ||||||
Components | FORMYL-COENZYME A TRANSFERASE | ||||||
Keywords | TRANSFERASE / CLASS III COA TRANSFERASE | ||||||
Function / homology | Function and homology information formyl-CoA transferase / formyl-CoA transferase activity / oxalate catabolic process / cytoplasm Similarity search - Function | ||||||
Biological species | OXALOBACTER FORMIGENES (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å | ||||||
Authors | Toyota, C.G. / Berthold, C.L. / Gruez, A. / Jonsson, S. / Lindqvist, Y. / Cambillau, C. / Richards, N.G.J. | ||||||
Citation | Journal: J.Bacteriol. / Year: 2008 Title: Differential Substrate Specificity and Kinetic Behavior of Escherichia Coli Yfdw and Oxalobacter Formigenes Formyl Coenzyme a Transferase. Authors: Toyota, C.G. / Berthold, C.L. / Gruez, A. / Jonsson, S. / Lindqvist, Y. / Cambillau, C. / Richards, N.G.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2vjp.cif.gz | 194.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2vjp.ent.gz | 154.5 KB | Display | PDB format |
PDBx/mmJSON format | 2vjp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vj/2vjp ftp://data.pdbj.org/pub/pdb/validation_reports/vj/2vjp | HTTPS FTP |
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-Related structure data
Related structure data | 2vjqC 1p5hS S: Starting model for refinement C: citing same article (ref.) |
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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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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (0.83856, -0.46616, -0.28199), Vector: |
-Components
#1: Protein | Mass: 47323.824 Da / Num. of mol.: 2 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) OXALOBACTER FORMIGENES (bacteria) / Plasmid: PET-9A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O06644, formyl-CoA transferase #2: Chemical | ChemComp-NA / | #3: Water | ChemComp-HOH / | Compound details | ENGINEERED | Sequence details | ACCORDING TO THE DEPOSITORS OF THIS ENTRY, THE SEQADV LISTED BELOW IS DUE TO AN ERROR IN THE ...ACCORDING TO THE DEPOSITORS | |
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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: 2.72 Å3/Da / Density % sol: 54 % / Description: NONE |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.873 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Sep 29, 2007 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.873 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→56.25 Å / Num. obs: 80837 / % possible obs: 97.9 % / Observed criterion σ(I): 2 / Redundancy: 4.2 % / Rmerge(I) obs: 0.13 / Net I/σ(I): 8.8 |
Reflection shell | Resolution: 1.95→2.06 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.53 / Mean I/σ(I) obs: 2.7 / % possible all: 99.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1P5H Resolution: 1.95→30 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.93 / SU B: 2.936 / SU ML: 0.086 / Cross valid method: THROUGHOUT / ESU R: 0.135 / ESU R Free: 0.127 / Stereochemistry target values: MAXIMUM LIKELIHOOD / 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: 15.1 Å2
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Refinement step | Cycle: LAST / Resolution: 1.95→30 Å
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