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- PDB-3b6d: Crystal Structure of Streptomyces Cholesterol Oxidase H447Q/E361Q... -

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Basic information

Entry
Database: PDB / ID: 3b6d
TitleCrystal Structure of Streptomyces Cholesterol Oxidase H447Q/E361Q mutant (1.2A)
ComponentsCholesterol oxidase
KeywordsOXIDOREDUCTASE / FLAVOENZYME / FLAVIN / FLAVIN ACTIVATION / CHOLESTEROL OXIDASE / 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
: / 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 / Twin arginine translocation (Tat) signal profile. ...: / 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 / 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 / FOURIER SYNTHESIS / Resolution: 1.2 Å
AuthorsLyubimov, A.Y. / 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 29, 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)55,8413
Polymers54,9591
Non-polymers8832
Water10,088560
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)51.300, 73.140, 63.140
Angle α, β, γ (deg.)90.00, 105.05, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Cholesterol oxidase / CHOD


Mass: 54958.676 Da / Num. of mol.: 1 / Mutation: H447Q/E361Q
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 / Gene: choA / Plasmid: PCO202 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)PLYSS / References: UniProt: P12676, cholesterol oxidase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-FAE / FLAVIN-N7 PROTONATED-ADENINE DINUCLEOTIDE


Mass: 786.558 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H34N9O15P2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 560 / 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: 2.08 Å3/Da / Density % sol: 40.9 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.2
Details: 10% PEG 8000, 75mM MnSO4, 100mM CACODYLATE pH 5.2, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5 Å / Relative weight: 1
ReflectionResolution: 1.2→60.97 Å / Num. obs: 132078 / % possible obs: 94.1 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 11.9
Reflection shellResolution: 1.2→1.22 Å / Redundancy: 1.3 % / Rmerge(I) obs: 0.196 / Mean I/σ(I) obs: 3.2 / % possible all: 74.5

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Processing

Software
NameClassification
REFMACrefinement
SHELXL-97refinement
CrystalCleardata collection
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB ENTRY 1MXT; ADP, WATERS, LIGANDS AND ACTIVE SITE SIDECHAINS REMOVED FROM STARTING MODEL

1mxt


Resolution: 1.2→38.03 Å / Num. parameters: 43986 / Num. restraintsaints: 62007 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.172 6605 5 %RANDOM
Rwork0.1321 ---
all0.133 ---
obs0.1321 132057 94.1 %-
Refine analyzeNum. disordered residues: 73 / Occupancy sum hydrogen: 3714 / Occupancy sum non hydrogen: 4427.84
Refinement stepCycle: LAST / Resolution: 1.2→38.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3819 0 58 560 4437
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_planes0.0316
X-RAY DIFFRACTIONs_zero_chiral_vol0.068
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.075
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.02
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.004
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.04
X-RAY DIFFRACTIONs_approx_iso_adps0.094

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