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- PDB-2vjo: Formyl-CoA transferase mutant variant Q17A with aspartyl-CoA thio... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2vjo | ||||||
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Title | Formyl-CoA transferase mutant variant Q17A with aspartyl-CoA thioester intermediates and oxalate | ||||||
![]() | FORMYL-COENZYME A TRANSFERASE | ||||||
![]() | TRANSFERASE / CYTOPLASM / CLASS III COA TRANSFERASE | ||||||
Function / homology | ![]() formyl-CoA transferase / formyl-CoA transferase activity / oxalate catabolic process / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Berthold, C.L. / Toyota, C.G. / Richards, N.G.J. / Lindqvist, Y. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 186.7 KB | Display | ![]() |
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PDB format | ![]() | 148.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 990.8 KB | Display | ![]() |
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Full document | ![]() | 1001.2 KB | Display | |
Data in XML | ![]() | 36.6 KB | Display | |
Data in CIF | ![]() | 52.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2vjkC ![]() 2vjlC ![]() 2vjmC ![]() 2vjnC ![]() 1p5hS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.86504, -0.494, -0.08759), Vector: |
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Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 47305.809 Da / Num. of mol.: 2 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Non-polymers , 5 types, 446 molecules ![](data/chem/img/COA.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/OXL.gif)
![](data/chem/img/EPE.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/OXL.gif)
![](data/chem/img/EPE.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | #4: Chemical | ChemComp-OXL / | #5: Chemical | ChemComp-EPE / | #6: Water | ChemComp-HOH / | |
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-Details
Compound details | ENGINEEREDSequence 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: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.86 Å3/Da / Density % sol: 56.7 % / Description: NONE |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Oct 4, 2007 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.037 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→41.3 Å / Num. obs: 57462 / % possible obs: 99.5 % / Observed criterion σ(I): 2 / Redundancy: 3.2 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 9.3 |
Reflection shell | Resolution: 2.2→2.32 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.57 / Mean I/σ(I) obs: 1.9 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1P5H Resolution: 2.2→30 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.903 / SU B: 5.752 / SU ML: 0.148 / Cross valid method: THROUGHOUT / ESU R: 0.245 / ESU R Free: 0.202 / 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: 32.86 Å2
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Refinement step | Cycle: LAST / Resolution: 2.2→30 Å
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Refine LS restraints |
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