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- PDB-1coy: CRYSTAL STRUCTURE OF CHOLESTEROL OXIDASE COMPLEXED WITH A STEROID... -

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Basic information

Entry
Database: PDB / ID: 1coy
TitleCRYSTAL STRUCTURE OF CHOLESTEROL OXIDASE COMPLEXED WITH A STEROID SUBSTRATE. IMPLICATIONS FOR FAD DEPENDENT ALCOHOL OXIDASES
ComponentsCHOLESTEROL OXIDASE
KeywordsOXIDOREDUCTASE(OXYGEN RECEPTOR)
Function / homology
Function and homology information


cholesterol oxidase / cholesterol oxidase activity / steroid Delta-isomerase / steroid Delta-isomerase activity / cholesterol catabolic process / flavin adenine dinucleotide binding / extracellular region
Similarity search - Function
: / GMC oxidoreductase, C-terminal / Cholesterol Oxidase; domain 2 / Cholesterol Oxidase; domain 2 / GMC oxidoreductases signature 1. / Glucose-methanol-choline oxidoreductase, N-terminal / GMC oxidoreductase / Glucose-methanol-choline oxidoreductase, C-terminal / GMC oxidoreductase / FAD/NAD(P)-binding domain ...: / GMC oxidoreductase, C-terminal / Cholesterol Oxidase; domain 2 / Cholesterol Oxidase; domain 2 / GMC oxidoreductases signature 1. / Glucose-methanol-choline oxidoreductase, N-terminal / GMC oxidoreductase / Glucose-methanol-choline oxidoreductase, C-terminal / GMC oxidoreductase / FAD/NAD(P)-binding domain / FAD/NAD(P)-binding domain / Twin arginine translocation (Tat) signal profile. / Twin-arginine translocation pathway, signal sequence / 3-Layer(bba) Sandwich / FAD/NAD(P)-binding domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
3-BETA-HYDROXY-5-ANDROSTEN-17-ONE / FLAVIN-ADENINE DINUCLEOTIDE / Cholesterol oxidase
Similarity search - Component
Biological speciesBrevibacterium sterolicum (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 1.8 Å
AuthorsLi, J. / Vrielink, A. / Brick, P. / Blow, D.M.
Citation
Journal: Biochemistry / Year: 1993
Title: Crystal structure of cholesterol oxidase complexed with a steroid substrate: implications for flavin adenine dinucleotide dependent alcohol oxidases.
Authors: Li, J. / Vrielink, A. / Brick, P. / Blow, D.M.
#1: Journal: J.Mol.Biol. / Year: 1991
Title: Crystal Structure of Cholesterol Oxidase from Brevibacterium Sterolicum Refined at 1.8 Angstroms Resolution
Authors: Vrielink, A. / Lloyd, L.F. / Blow, D.M.
#2: Journal: Gene / Year: 1991
Title: Sequence of Gene Chob Encoding Cholesterol Oxidase of Brevibacterium Sterolicum: Comparison with Choa of Streptomyces Sp. Sa-Coo
Authors: Ohta, T. / Fujishiro, K. / Yamaguchi, K. / Tamura, Y. / Aisaka, K. / Uwajima, T. / Hasegawa, M.
History
DepositionJun 14, 1993Processing site: BNL
Revision 1.0Oct 31, 1993Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 29, 2017Group: Derived calculations / Other
Category: pdbx_database_status / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site
Revision 1.4Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CHOLESTEROL OXIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,9663
Polymers54,8921
Non-polymers1,0742
Water7,638424
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)67.930, 84.230, 87.930
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein CHOLESTEROL OXIDASE


Mass: 54891.742 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Brevibacterium sterolicum (bacteria) / References: UniProt: P22637, cholesterol oxidase
#2: Chemical ChemComp-AND / 3-BETA-HYDROXY-5-ANDROSTEN-17-ONE


Mass: 288.424 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H28O2
#3: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 424 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsTHE STRUCTURE CONTAINS AN FAD COFACTOR IN THE REDUCED FORM. THE FLAVIN RING SYSTEM OF THE FAD ...THE STRUCTURE CONTAINS AN FAD COFACTOR IN THE REDUCED FORM. THE FLAVIN RING SYSTEM OF THE FAD MOLECULE ADOPTS A SLIGHTLY TWISTED CONFORMATION.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.29 Å3/Da / Density % sol: 46.3 %
Crystal grow
*PLUS
Temperature: 18 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
120 mg/mlprotein1drop
20.5-0.65 Msodium/potassium phosphate1drop
31.3 Msodium/potassium phosphate1reservoir

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 1.8 Å / Num. obs: 46169 / % possible obs: 96.3 % / Num. measured all: 192439 / Rmerge(I) obs: 0.066

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementResolution: 1.8→10 Å / Rfactor Rwork: 0.159 / Rfactor obs: 0.159
Refinement stepCycle: LAST / Resolution: 1.8→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3771 0 74 424 4269
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.01
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.35
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Num. reflection obs: 44943 / Rfactor obs: 0.159
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 16.6 Å2
Refine LS restraints
*PLUS
Type: x_angle_d / Dev ideal: 1.35

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