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Yorodumi- PDB-2ji7: X-ray structure of Oxalyl-CoA decarboxylase with covalent reactio... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2ji7 | ||||||
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Title | X-ray structure of Oxalyl-CoA decarboxylase with covalent reaction intermediate | ||||||
Components | OXALYL-COA DECARBOXYLASE | ||||||
Keywords | LYASE / FLAVOPROTEIN / DECARBOXYLASE / OXALATE DEGRADATION / INTERMEDIATE COMPLEX / THIAMIN DIPHOSPHATE-DEPENDENT / THIAMINE PYROPHOSPHATE / NON- OXIDATIVE DECARBOXYLASE | ||||||
Function / homology | Function and homology information 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 | OXALOBACTER FORMIGENES (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.82 Å | ||||||
Authors | Berthold, C.L. / Toyota, C.G. / Moussatche, P. / Wood, M.D. / Leeper, F. / Richards, N.G.J. / Lindqvist, Y. | ||||||
Citation | Journal: Structure / Year: 2007 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2ji7.cif.gz | 256.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2ji7.ent.gz | 203.5 KB | Display | PDB format |
PDBx/mmJSON format | 2ji7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2ji7_validation.pdf.gz | 3.1 MB | Display | wwPDB validaton report |
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Full document | 2ji7_full_validation.pdf.gz | 3 MB | Display | |
Data in XML | 2ji7_validation.xml.gz | 55.3 KB | Display | |
Data in CIF | 2ji7_validation.cif.gz | 82.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ji/2ji7 ftp://data.pdbj.org/pub/pdb/validation_reports/ji/2ji7 | HTTPS FTP |
-Related structure data
Related structure data | 2ji6C 2ji8C 2ji9C 2jibC 2c31S 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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Components on special symmetry positions |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-1, 0.002592, 0.000765), Vector: |
-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.) OXALOBACTER FORMIGENES (bacteria) / Plasmid: PET9A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P40149, oxalyl-CoA decarboxylase |
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-Non-polymers , 6 types, 1199 molecules
#2: Chemical | #3: Chemical | #4: Chemical | #5: Chemical | #6: Chemical | ChemComp-B3P / #7: Water | ChemComp-HOH / | |
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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: 2.9 Å3/Da / Density % sol: 57.2 % / Description: NONE |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.976 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Sep 9, 2006 / Details: TOROIDAL MIRROR |
Radiation | Monochromator: THIN DIAMOND DOUBLE CRYSTALS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.976 Å / Relative weight: 1 |
Reflection | Resolution: 1.82→76 Å / Num. obs: 124184 / % possible obs: 99.2 % / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Biso Wilson estimate: 18.66 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 10.2 |
Reflection shell | Resolution: 1.82→1.92 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 2 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2C31 Resolution: 1.82→30 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.962 / SU B: 4.325 / SU ML: 0.07 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.099 / ESU R Free: 0.095 / 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: 19.91 Å2
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Refinement step | Cycle: LAST / Resolution: 1.82→30 Å
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Refine LS restraints |
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