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- PDB-2vjm: Formyl-CoA transferase with aspartyl-formyl anhydide intermediate -
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Open data
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Basic information
Entry | Database: PDB / ID: 2vjm | ||||||
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Title | Formyl-CoA transferase with aspartyl-formyl anhydide intermediate | ||||||
![]() | (FORMYL-COENZYME A ...) x 2 | ||||||
![]() | 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 | ![]() | 197.7 KB | Display | ![]() |
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PDB format | ![]() | 155.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 795.2 KB | Display | ![]() |
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Full document | ![]() | 806 KB | Display | |
Data in XML | ![]() | 39.9 KB | Display | |
Data in CIF | ![]() | 59.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2vjkC ![]() 2vjlC ![]() 2vjnC ![]() 2vjoC ![]() 1p5hS C: citing same article ( S: Starting model for refinement |
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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: (-0.88368, -0.46295, -0.06923), Vector: |
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Components
-FORMYL-COENZYME A ... , 2 types, 2 molecules AB
#1: Protein | Mass: 47362.859 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Protein | Mass: 47390.867 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
-Non-polymers , 4 types, 760 molecules ![](data/chem/img/COA.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/EPE.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/EPE.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | #4: Chemical | ChemComp-NA / | #5: Chemical | ChemComp-EPE / | #6: Water | ChemComp-HOH / | |
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-Details
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: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.7 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: ![]() ![]() ![]() |
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: 1.87→44.9 Å / Num. obs: 89577 / % possible obs: 97.1 % / Observed criterion σ(I): 2 / Redundancy: 4.1 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 15.9 |
Reflection shell | Resolution: 1.87→1.97 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 4.2 / % possible all: 81.1 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1P5H Resolution: 1.89→30 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.94 / SU B: 2.413 / SU ML: 0.074 / Cross valid method: THROUGHOUT / ESU R: 0.122 / ESU R Free: 0.116 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUE A 139 HAS BEEN MODELLED WITH ZERO OCCUPANCY DUE TO DISORDER
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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: 20.01 Å2
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Refinement step | Cycle: LAST / Resolution: 1.89→30 Å
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Refine LS restraints |
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