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- PDB-3b3r: Crystal structure of Streptomyces cholesterol oxidase H447Q/E361Q... -

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Basic information

Entry
Database: PDB / ID: 3b3r
TitleCrystal structure of Streptomyces cholesterol oxidase H447Q/E361Q mutant bound to glycerol (0.98A)
ComponentsCholesterol oxidase
KeywordsOXIDOREDUCTASE / flavoenzyme / flavin / cholesterol oxidase / covalently-modified flavin / Cholesterol metabolism / FAD / Flavoprotein / Lipid metabolism / Secreted / 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
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 / Twin arginine translocation (Tat) signal profile. / Twin-arginine translocation pathway, signal sequence / FAD/NAD(P)-binding domain ...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 / Twin arginine translocation (Tat) signal profile. / Twin-arginine translocation pathway, signal sequence / FAD/NAD(P)-binding domain / FAD/NAD(P)-binding domain / 3-Layer(bba) Sandwich / FAD/NAD(P)-binding domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
FLAVIN-N7 PROTONATED-ADENINE DINUCLEOTIDE / Cholesterol oxidase
Similarity search - Component
Biological speciesStreptomyces sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 0.98 Å
AuthorsLyubimov, A.Y. / Heard, K. / Tang, H. / Sampson, N.S. / Vrielink, A.
CitationJournal: Protein Sci. / Year: 2007
Title: Distortion of flavin geometry is linked to ligand binding in cholesterol oxidase
Authors: Lyubimov, A.Y. / Heard, K. / Tang, H. / Sampson, N.S. / Vrielink, A.
History
DepositionOct 22, 2007Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 18, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Nov 10, 2021Group: Database references / Derived calculations / Category: 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
Revision 1.3Nov 1, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cholesterol oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,3727
Polymers55,1171
Non-polymers1,2556
Water13,583754
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)51.314, 73.643, 63.275
Angle α, β, γ (deg.)90.00, 104.98, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Cholesterol oxidase / / CHOD


Mass: 55116.832 Da / Num. of mol.: 1 / Mutation: E361Q/H447Q
Source method: isolated from a genetically manipulated source
Details: FAD COFACTOR NON-COVALENTLY BOUND TO THE ENZYME / Source: (gene. exp.) Streptomyces sp. (bacteria) / Strain: SA-COO / Plasmid: PCO202 / Production host: Escherichia coli (E. coli) / Strain (production host): BL-21 pLys(S) / References: UniProt: P12676, cholesterol oxidase
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-FAE / FLAVIN-N7 PROTONATED-ADENINE DINUCLEOTIDE / Flavin adenine dinucleotide


Mass: 786.558 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H34N9O15P2
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 754 / Source method: isolated from a natural source / Formula: H2O

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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: 2.1 Å3/Da / Density % sol: 41.3 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.2
Details: 10% PEG 8000, 75mM magnesium sulfate, 100mM cacodylate, pH 5.2, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.93 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Details: vertical focusing mirror
RadiationMonochromator: crystal Si(311) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.93 Å / Relative weight: 1
ReflectionResolution: 0.98→38.11 Å / Num. all: 246315 / Num. obs: 259284 / % possible obs: 99.9 % / Redundancy: 3.75 % / Biso Wilson estimate: 6.9 Å2 / Rmerge(I) obs: 0.066 / Net I/σ(I): 7.8
Reflection shellResolution: 0.98→1.02 Å / Redundancy: 3.38 % / Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 2.1 / % possible all: 99.9

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Processing

Software
NameVersionClassificationNB
d*TREKdata scaling
SHELXrefinement
PDB_EXTRACT3data extraction
HKL-2000data collection
d*TREKdata reduction
REFMACphasing
SHELXL-97refinement
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB ENTRY 1MXT; ADP, HETEROATOMS, WATERS AND ACTIVE SITE SIDECHAINS REMOVED FROM STARTING MODEL

1mxt


Resolution: 0.98→34.4 Å / Num. parameters: 48221 / Num. restraintsaints: 68015 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: ANISOTROPIC REFINEMENT REDUCED FREE R (NO CUTOFF) BY ?
RfactorNum. reflection% reflectionSelection details
Rfree0.1589 12969 5.3 %RANDOM
all0.1291 246315 --
obs0.1292 -94.9 %-
Solvent computationSolvent model: MOEWS & KRETSINGER, J.MOL.BIOL.91(1973)201-228
Displacement parametersBiso mean: 13.885 Å2
Refine analyzeNum. disordered residues: 127 / Occupancy sum hydrogen: 3342.12 / Occupancy sum non hydrogen: 4503.74
Refinement stepCycle: LAST / Resolution: 0.98→34.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3839 0 81 754 4674
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.012
X-RAY DIFFRACTIONs_angle_d0.029
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.033
X-RAY DIFFRACTIONs_zero_chiral_vol0.082
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.092
X-RAY DIFFRACTIONs_anti_bump_dis_restr0
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.005
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.042
X-RAY DIFFRACTIONs_approx_iso_adps0.094

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