+Open data
-Basic information
Entry | Database: PDB / ID: 2vjn | ||||||
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Title | Formyl-CoA transferase mutant variant G260A | ||||||
Components | FORMYL-COENZYME A TRANSFERASE | ||||||
Keywords | TRANSFERASE / CYTOPLASM / 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: 2 Å | ||||||
Authors | Berthold, C.L. / Toyota, C.G. / Richards, N.G.J. / Lindqvist, Y. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2008 Title: Reinvestigation of the Catalytic Mechanism of Formyl-Coa Transferase, a Class III Coa-Transferase. Authors: Berthold, C.L. / Toyota, C.G. / Richards, N.G.J. / Lindqvist, Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2vjn.cif.gz | 192.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2vjn.ent.gz | 153.2 KB | Display | PDB format |
PDBx/mmJSON format | 2vjn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2vjn_validation.pdf.gz | 443.1 KB | Display | wwPDB validaton report |
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Full document | 2vjn_full_validation.pdf.gz | 450.5 KB | Display | |
Data in XML | 2vjn_validation.xml.gz | 39.7 KB | Display | |
Data in CIF | 2vjn_validation.cif.gz | 61.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vj/2vjn ftp://data.pdbj.org/pub/pdb/validation_reports/vj/2vjn | HTTPS FTP |
-Related structure data
Related structure data | 2vjkC 2vjlC 2vjmC 2vjoC 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: (0.25681, 0.23347, 0.93784), Vector: |
-Components
#1: Protein | Mass: 47376.887 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-EPE / | #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: 2.16 Å3/Da / Density % sol: 42.6 % / 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: 2→48.6 Å / Num. obs: 63094 / % possible obs: 99.6 % / Observed criterion σ(I): 2 / Redundancy: 3.3 % / Rmerge(I) obs: 0.15 / Net I/σ(I): 7.2 |
Reflection shell | Resolution: 2→2.11 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 2.5 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1P5H Resolution: 2→30 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.911 / SU B: 3.595 / SU ML: 0.102 / Cross valid method: THROUGHOUT / ESU R: 0.174 / ESU R Free: 0.156 / 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: 10.13 Å2
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Refinement step | Cycle: LAST / Resolution: 2→30 Å
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Refine LS restraints |
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