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- PDB-2ji8: X-ray structure of Oxalyl-CoA decarboxylase in complex with Formy... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2ji8 | ||||||
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Title | X-ray structure of Oxalyl-CoA decarboxylase in complex with Formyl- CoA | ||||||
![]() | OXALYL-COA DECARBOXYLASE | ||||||
![]() | LYASE / OXALATE DEGRADATION / THIAMINE PYROPHOSPHATE / NON- OXIDATIVE DECARBOXYLASE / FLAVOPROTEIN / DECARBOXYLASE / PRODUCT COMPLEX / THIAMIN DIPHOSPHATE-DEPENDENT | ||||||
Function / homology | ![]() oxalyl-CoA decarboxylase / oxalyl-CoA decarboxylase activity / oxalate catabolic process / fatty acid alpha-oxidation / thiamine pyrophosphate binding / ADP binding / peroxisome / magnesium ion binding / identical protein binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Berthold, C.L. / Toyota, C.G. / Moussatche, P. / Wood, M.D. / Leeper, F. / Richards, N.G.J. / Lindqvist, Y. | ||||||
![]() | ![]() Title: Crystallographic Snapshots of Oxalyl-Coa Decarboxylase Give Insights Into Catalysis by Nonoxidative Thdp-Dependent Decarboxylases Authors: Berthold, C.L. / Toyota, C.G. / Moussatche, P. / Wood, M.D. / Leeper, F. / 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 | ![]() | 237.8 KB | Display | ![]() |
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PDB format | ![]() | 188.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 2.1 MB | Display | ![]() |
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Full document | ![]() | 2.1 MB | Display | |
Data in XML | ![]() | 25.2 KB | Display | |
Data in CIF | ![]() | 40.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2ji6C ![]() 2ji7C ![]() 2ji9C ![]() 2jibC ![]() 2c31S 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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1 | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-1, 0.00169, -0.001128), Vector: |
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Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 60749.867 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Non-polymers , 6 types, 624 molecules ![](data/chem/img/TPP.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/ADP.gif)
![](data/chem/img/FYN.gif)
![](data/chem/img/PGE.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/ADP.gif)
![](data/chem/img/FYN.gif)
![](data/chem/img/PGE.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | #4: Chemical | #5: Chemical | #6: Chemical | #7: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.9 Å3/Da / Density % sol: 58.2 % / Description: NONE |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC CCD / Detector: CCD / Date: Sep 9, 2006 / Details: TOROIDAL MIRROR |
Radiation | Monochromator: DIAMOND (111), GE(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.931 Å / Relative weight: 1 |
Reflection | Resolution: 2.05→51.9 Å / Num. obs: 298530 / % possible obs: 98.6 % / Redundancy: 3.4 % / Biso Wilson estimate: 24.1 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 9.3 |
Reflection shell | Resolution: 2.05→2.16 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.3 / Mean I/σ(I) obs: 2.2 / % possible all: 97.5 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2C31 Resolution: 2.15→25 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.941 / SU B: 11.342 / SU ML: 0.157 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.208 / ESU R Free: 0.179 / 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: 24.3 Å2
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Refinement step | Cycle: LAST / Resolution: 2.15→25 Å
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Refine LS restraints |
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