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- PDB-2jbv: Crystal structure of choline oxidase reveals insights into the ca... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2jbv | ||||||
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Title | Crystal structure of choline oxidase reveals insights into the catalytic mechanism | ||||||
![]() | CHOLINE OXIDASE | ||||||
![]() | OXIDOREDUCTASE / ALCOHOL OXIDATION / FLAVOENYZME OXIDASE / COVALENTLY LINKED FAD / ARTHROBACTER GLOBIFORMIS / C4A-ADDUCT / FLAVOPROTEIN / GLUCOSE-METHANOL-CHOLINE OXIDOREDUCTASE ENZYME SUPERFAMILY | ||||||
Function / homology | ![]() choline oxidase / choline:oxygen 1-oxidoreductase activity / glycine betaine biosynthetic process from choline / flavin adenine dinucleotide binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Lountos, G.T. / Fan, F. / Gadda, G. / Orville, A.M. | ||||||
![]() | ![]() Title: Role of Glu312 in Binding and Positioning of the Substrate for the Hydride Transfer Reaction in Choline Oxidase. Authors: Quaye, O. / Lountos, G.T. / Fan, F. / Orville, A.M. / Gadda, G. #1: Journal: Arch.Biochem.Biophys. / Year: 2004 Title: Cloning, Sequence Analysis, and Purification of Choline Oxidase from Arthrobacter Globiformis: A Bacterial Enzyme Involved in Osmotic Stress Tolerance Authors: Fan, F. / Ghanem, M. / Gadda, G. #2: Journal: Biochim.Biophys.Acta / Year: 2003 Title: Kinetic Mechanism of Choline Oxidase from Arthrobacter Globiformis Authors: Gadda, G. #3: Journal: Arch.Biochem.Biophys. / Year: 2004 Title: The Trimethylammonium Headgroup of Choline is a Major Determinant for Substrate Binding and Specificity in Choline Oxidase Authors: Gadda, G. / Powell, N.L. / Menon, P. #4: Journal: J.Am.Chem.Soc. / Year: 2005 Title: On the Catalytic Mechanism of Choline Oxidase Authors: Fan, F. / Gadda, G. #5: Journal: Biochemistry / Year: 2005 Title: On the Catalytic Role of the Conserved Active Site Residue His466 of Choline Oxidase Authors: Ghanem, M. / Gadda, G. #6: Journal: Biochemistry / Year: 2006 Title: Effects of Reversing the Protein Positive Charge in the Proximity of the Flavin N(1) Locus of Choline Oxidase Authors: Ghanem, M. / Gadda, G. | ||||||
History |
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Remark 700 | SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED. |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 238.4 KB | Display | ![]() |
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PDB format | ![]() | 189.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 944.7 KB | Display | ![]() |
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Full document | ![]() | 959.7 KB | Display | |
Data in XML | ![]() | 49.5 KB | Display | |
Data in CIF | ![]() | 74.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1cf3S 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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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 59898.754 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: COVALENT LINKAGE BETWEEN C8M ATOM OF FAO AND NE2 ATOM OF HIS99 OF CHOLINE OXIDASE Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | #3: Chemical | #4: Chemical | ChemComp-UNX / #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.5 Å3/Da / Density % sol: 50 % / Description: NONE |
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Crystal grow | Temperature: 296 K / pH: 8.5 Details: 4.9 MG/ML CHOLINE OXIDASE, 100 MM BIS TRIS PROPANE PH 8.5, 1.2 M AMMONIUM SULFATE, 10% V/V DMSO, 23 C CRYSTALS WERE CRYOPROTECTED BY SOAKING FOR 2 MIN IN 3.4 M SODIUM MALONATE PH 7 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Mar 16, 2005 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.86→1.91 Å / Num. obs: 97546 / % possible obs: 92.3 % / Observed criterion σ(I): 2 / Redundancy: 3.9 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 17.7 |
Reflection shell | Resolution: 1.86→1.91 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.32 / Mean I/σ(I) obs: 2.3 / % possible all: 63.2 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1CF3 Resolution: 1.86→50 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.943 / SU B: 2.752 / SU ML: 0.083 / Cross valid method: THROUGHOUT / ESU R: 0.134 / ESU R Free: 0.13 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUES 528-546 WERE NOT LOCATED IN THE EXPERIMENT
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 23.14 Å2
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Refinement step | Cycle: LAST / Resolution: 1.86→50 Å
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