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Open data
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Basic information
Entry | Database: PDB / ID: 1i19 | ||||||
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Title | CRYSTAL STRUCTURE OF CHOLESTEROL OXIDASE FROM B.STEROLICUM | ||||||
![]() | CHOLESTEROL OXIDASE | ||||||
![]() | OXIDOREDUCTASE / MIX ALPHA BETA / covalent FAD / Flavoenzyme | ||||||
Function / homology | ![]() L-gulono-1,4-lactone dehydrogenase activity / D-arabinono-1,4-lactone oxidase activity / FAD binding / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Coulombe, R. / Yue, K.Q. / Ghisla, S. / Vrielink, A. | ||||||
![]() | ![]() Title: Oxygen access to the active site of cholesterol oxidase through a narrow channel is gated by an Arg-Glu pair. Authors: Coulombe, R. / Yue, K.Q. / Ghisla, S. / Vrielink, A. #1: ![]() Title: Crystallization and Preliminary X-Ray Analysis of Cholesterol Oxidase from Brevibacterium sterolicum Containing Covalently Bound FAD Authors: Croteau, N. / Vrielink, A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 245.3 KB | Display | ![]() |
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PDB format | ![]() | 202.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
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
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 61575.082 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: COVALENT FAD / Source: (gene. exp.) ![]() ![]() ![]() |
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-Non-polymers , 5 types, 1023 molecules ![](data/chem/img/EDO.gif)
![](data/chem/img/FAD.gif)
![](data/chem/img/MN.gif)
![](data/chem/img/CAC.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/FAD.gif)
![](data/chem/img/MN.gif)
![](data/chem/img/CAC.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-EDO / #3: Chemical | #4: Chemical | #5: Chemical | ChemComp-CAC / | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.99 Å3/Da / Density % sol: 58.81 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, hanging drop / pH: 5.2 Details: PEG 8K, MnSO4, NaCacodylate, pH 5.2, VAPOR DIFFUSION, HANGING DROP, temperature 290K | ||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 22 ℃ / pH: 7 / Details: Croteau, N., (1996) J.STRUCT.BIOL., 116, 317. | ||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Aug 27, 1999 |
Radiation | Monochromator: crystals Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→100 Å / Num. all: 554010 / Num. obs: 550182 / % possible obs: 94.8 % / Observed criterion σ(I): 1 / Redundancy: 3.7 % / Biso Wilson estimate: 17.8 Å2 / Rmerge(I) obs: 0.065 / Net I/σ(I): 17.6 |
Reflection shell | Resolution: 1.7→1.74 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.377 / Mean I/σ(I) obs: 2.7 / Num. unique all: 7196 / % possible all: 68.4 |
Reflection | *PLUS Num. obs: 150202 / Num. measured all: 550182 |
Reflection shell | *PLUS % possible obs: 68.4 % |
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Processing
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Refinement | Method to determine structure: ![]() Details: The following atoms have occupancies set to 0.00 or 0.50 because of weak electron density: CG1 and CG2 of VAL 349 chains A and B have occupancy set to 0.00; CG, OD1, ND2 of ASN A 65, all ...Details: The following atoms have occupancies set to 0.00 or 0.50 because of weak electron density: CG1 and CG2 of VAL 349 chains A and B have occupancy set to 0.00; CG, OD1, ND2 of ASN A 65, all atoms of PRO A 330, CG, OD1, OD2 of ASP A 544, CG, OD1, ND2 of ASN B 65, and CG, OD1, OD2 of ASP B 179 have occupancy set to 0.50.
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 45.73 Å2 / ksol: 0.368 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 19.8 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.7→36.91 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.7→1.81 Å / Rfactor Rfree error: 0.006 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: CNS / Version: 0.9 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS σ(F): 0 / % reflection Rfree: 10 % / Rfactor obs: 0.182 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 19.8 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.264 / % reflection Rfree: 10 % / Rfactor Rwork: 0.244 |