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- PDB-1b4v: CHOLESTEROL OXIDASE FROM STREPTOMYCES -

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Basic information

Entry
Database: PDB / ID: 1b4v
TitleCHOLESTEROL OXIDASE FROM STREPTOMYCES
ComponentsPROTEIN (CHOLESTEROL OXIDASE)
KeywordsOXIDOREDUCTASE / FLAVOENZYME / STEROID METABOLISM
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 speciesStreptomyces sp. (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsVrielink, A. / Yue, Q.K.
CitationJournal: Biochemistry / Year: 1999
Title: Crystal structure determination of cholesterol oxidase from Streptomyces and structural characterization of key active site mutants.
Authors: Yue, Q.K. / Kass, I.J. / Sampson, N.S. / Vrielink, A.
History
DepositionDec 30, 1998Deposition site: BNL / Processing site: RCSB
Revision 1.0Jan 6, 1999Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Aug 9, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: PROTEIN (CHOLESTEROL OXIDASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,7552
Polymers54,9701
Non-polymers7861
Water11,962664
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)51.304, 72.964, 63.022
Angle α, β, γ (deg.)90.00, 105.09, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein PROTEIN (CHOLESTEROL OXIDASE)


Mass: 54969.676 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: FAD COFACTOR NON-COVALENTLY BOUND TO THE ENZYME / Source: (natural) Streptomyces sp. (bacteria) / References: UniProt: P12676, 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.: 664 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE SEQUENCE OF CHOLESTEROL OXIDASE FROM STREPTOMYCES SP FOUND IN THE SEQUENCE DATA BASE IS A ...THE SEQUENCE OF CHOLESTEROL OXIDASE FROM STREPTOMYCES SP FOUND IN THE SEQUENCE DATA BASE IS A PRECURSOR FORM OF THE ENZYME. THE MATURE ENZYME RUNS FROM RESIDUES 43 - 546. THE NUMBERING OF THE RESIDUES DIFFERS FROM THAT IN THE DATABASE DUE TO THIS DESCREPANCY IN THE SEQUENCE. IN ADDITION, THE NUMBERING HAS BEEN ADJUSTED TO CONFORM TO THAT FOUND IN THE STRUCTURE OF CHOLESTEROL OXIDASE FROM BREVIBACTERIUM STEROLICUM (ACCESSION CODE 3COX). THIS CHANGE IN THE NUMBERING SCHEME FACILITATES COMPARISONS OF THE TWO STRUCTURES.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.2 Å3/Da / Density % sol: 44 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 5.2
Details: PRECIPITANT CONDITIONS: 10- 12% PEG 8000, 100MM SODIUM CACODYLATE PH 5.2, 75MM MNSO4 PROTEIN CONCENTRATION 8.5MG/ML, VAPOR DIFFUSION, HANGING DROP
Crystal grow
*PLUS
Temperature: 17 ℃ / pH: 7
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
18.5 mg/mlprotein1drop
210 mMHEPES1drop
310-12 %(w/v)PEG80001reservoir
4100 mMsodium cacodylate1reservoir
575 mM1reservoirMnSO4

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Data collection

DiffractionMean temperature: 115 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: Oct 1, 1996
RadiationMonochromator: GRAPHITE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.5→22.3 Å / Num. obs: 62747 / % possible obs: 87.4 % / Redundancy: 6.4 % / Biso Wilson estimate: 14.9 Å2 / Rmerge(I) obs: 0.045 / Net I/σ(I): 27.5
Reflection shellResolution: 1.5→1.55 Å / Redundancy: 0.31 % / Rmerge(I) obs: 0.22 / Mean I/σ(I) obs: 2 / % possible all: 30.9
Reflection
*PLUS
Num. measured all: 402969

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Processing

Software
NameVersionClassification
AMoREphasing
X-PLOR3.843refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3COX

3cox


Resolution: 1.5→20 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 1000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.2 6343 10.1 %RANDOM
Rwork0.181 ---
obs0.181 62692 87.4 %-
Displacement parametersBiso mean: 12.4 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.18 Å0.16 Å
Luzzati d res low-5 Å
Luzzati sigma a0.14 Å0.15 Å
Refinement stepCycle: LAST / Resolution: 1.5→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3848 0 53 664 4565
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.006
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_deg1.4
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d24.9
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.28
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it0.91.5
X-RAY DIFFRACTIONx_mcangle_it1.312
X-RAY DIFFRACTIONx_scbond_it1.82
X-RAY DIFFRACTIONx_scangle_it2.732.5
LS refinement shellResolution: 1.5→1.57 Å / Rfactor Rfree error: 0.023 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.4099 312 10.1 %
Rwork0.4162 2784 -
obs--34.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2WATER.PARAMWATER.TOP
X-RAY DIFFRACTION3FAD.PARAM2FAD.TOP
Software
*PLUS
Name: X-PLOR / Version: 3.843 / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.5 Å / Lowest resolution: 20 Å / σ(F): 0 / % reflection Rfree: 10.1 % / Rfactor Rfree: 0.2
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 12.4 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_angle_deg1.4
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg24.9
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.28
X-RAY DIFFRACTIONx_mcbond_it1.5
X-RAY DIFFRACTIONx_scbond_it2
X-RAY DIFFRACTIONx_mcangle_it2
X-RAY DIFFRACTIONx_scangle_it2.5
LS refinement shell
*PLUS
Highest resolution: 1.5 Å / % reflection Rfree: 10.1 %

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