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- PDB-3cox: CRYSTAL STRUCTURE OF CHOLESTEROL OXIDASE COMPLEXED WITH A STEROID... -

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Basic information

Entry
Database: PDB / ID: 3cox
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
FLAVIN-ADENINE DINUCLEOTIDE / Cholesterol oxidase
Similarity search - Component
Biological speciesBrevibacterium sterolicum (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 1.8 Å
AuthorsVrielink, A. / Li, J. / 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
SupersessionOct 15, 1993ID: 1COX
Revision 1.0Oct 31, 1993Provider: repository / Type: Initial release
Revision 1.1Mar 25, 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 21, 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)55,6772
Polymers54,8921
Non-polymers7861
Water8,161453
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)67.720, 84.580, 88.130
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-FAD / FLAVIN-ADENINE DINUCLEOTIDE


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


Mass: 18.015 Da / Num. of mol.: 453 / Source method: isolated from a natural source / Formula: H2O
Compound detailsTHE STRUCTURE CONTAINS AN FAD COFACTOR IN THE OXIDIZED FORM. THE FLAVIN RING SYSTEM OF THE FAD ...THE STRUCTURE CONTAINS AN FAD COFACTOR IN THE OXIDIZED 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: 2.3 Å3/Da / Density % sol: 46.48 %
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

Reflection
*PLUS
Highest resolution: 1.8 Å / Num. obs: 46364 / % possible obs: 97.6 % / Num. measured all: 175309 / 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: 0.156 / Rfactor obs: 0.156 / σ(F): 0
Refinement stepCycle: LAST / Resolution: 1.8→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3738 0 53 453 4244
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.011
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_deg
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
Refinement
*PLUS
Highest resolution: 1.8 Å / Lowest resolution: 10 Å / Num. reflection all: 45729 / σ(F): 0 / Rfactor all: 0.156
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 19.4 Å2

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