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- PDB-4u2l: Dithionite reduced cholesterol in complex with sulfite -

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Basic information

Entry
Database: PDB / ID: 4u2l
TitleDithionite reduced cholesterol in complex with sulfite
ComponentsCholesterol oxidase
KeywordsOXIDOREDUCTASE / ISOMERASE / cholesterol oxidase / flavoenzymes / redox chemistry
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
Chem-SFD / Cholesterol oxidase
Similarity search - Component
Biological speciesStreptomyces sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.337 Å
AuthorsGolden, E.A. / Vrielink, A.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2014
Title: High-resolution structures of cholesterol oxidase in the reduced state provide insights into redox stabilization.
Authors: Golden, E. / Karton, A. / Vrielink, A.
History
DepositionJul 17, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 10, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 24, 2014Group: Database references
Revision 1.2Feb 4, 2015Group: Derived calculations
Revision 1.3Jun 1, 2016Group: Data collection
Revision 1.4Nov 22, 2017Group: Data collection / Derived calculations / Refinement description
Category: diffrn_source / pdbx_struct_oper_list / software
Item: _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation
Revision 1.5Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)56,9545
Polymers55,7991
Non-polymers1,1564
Water11,944663
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)51.375, 73.565, 63.431
Angle α, β, γ (deg.)90.000, 105.030, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Cholesterol oxidase / / CHOD / Cholesterol isomerase


Mass: 55798.543 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces sp. (bacteria) / Strain: SA-COO / Gene: choA / Production host: Escherichia coli (E. coli) / Variant (production host): BL21(DE3)
References: UniProt: P12676, cholesterol oxidase, steroid Delta-isomerase
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-SFD / (S)-10-((2S,3S,4R)-5-((S)-((S)-(((2R,3S,4R,5R)-5-(6-AMINO-9H-PURIN-9-YL)-3,4-DIHYDROXY-TETRAHYDROFURAN-2-YL)METHOXY)(HYDROXY)PHOSPHORYLOXY)(HYDROXY)PHOSPHORYLOXY)-2,3,4-TRIHYDROXYPENTYL)-7,8-DIMETHYL-2,4-DIOXO-2,3,4,4A-TETRAHYDROBENZO[G]PTERIDINE-5(10H)-SULFONIC ACID / N5-SULFONO FLAVIN-ADENINE DINUCLEOTIDE


Mass: 867.629 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H35N9O18P2S
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 663 / 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: 2.12 Å3/Da / Density % sol: 42.07 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.2 / Details: PEG 8000, manganese chloride, cacodylate / PH range: 5.2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 30, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.32→61.262 Å / Num. all: 100763 / Num. obs: 100763 / % possible obs: 94.2 % / Redundancy: 12 % / Biso Wilson estimate: 6.6 Å2 / Rpim(I) all: 0.115 / Rrim(I) all: 0.398 / Rsym value: 0.381 / Net I/av σ(I): 1.22 / Net I/σ(I): 12.3 / Num. measured all: 1209726
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRsym valueNet I/σ(I) obs% possible all
1.32-1.398.91.1660.68399594330.3721.166360.7
1.39-1.4812.60.9890.7185994147490.2880.9895.1100
1.48-1.5812.90.8090.8178380138310.2340.8096.6100
1.58-1.713.10.6980.9169086128990.20.6988.4100
1.7-1.8713.10.5831155435118940.1680.58310.9100
1.87-2.0912.60.4531.3134896107250.1330.45314.7100
2.09-2.4111.90.3641.511264094870.110.36418.6100
2.41-2.9511.20.3231.69013780500.10.32322.1100
2.95-4.1710.30.1892.36447462500.0610.18931100
4.17-19.97510.10.1283.23468934450.0420.12829.199

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Processing

Software
NameVersionClassification
PHENIXrefinement
SCALA3.3.20data scaling
PDB_EXTRACT3.14data extraction
PHASERphasing
RefinementStarting model: 1MXT

1mxt


Resolution: 1.337→19.975 Å / SU ML: 0.07 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 10.52 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1328 9945 10.08 %
Rwork0.097 88724 -
obs0.1006 98669 96.03 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 56.21 Å2 / Biso mean: 9.6697 Å2 / Biso min: 1.57 Å2
Refinement stepCycle: final / Resolution: 1.337→19.975 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3834 0 103 682 4619
Biso mean--5.35 20.41 -
Num. residues----499
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0114501
X-RAY DIFFRACTIONf_angle_d1.386102
X-RAY DIFFRACTIONf_chiral_restr0.09642
X-RAY DIFFRACTIONf_plane_restr0.008830
X-RAY DIFFRACTIONf_dihedral_angle_d12.7051653
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.3373-1.35251.816231.752569
1.3525-1.36840.33152930.24382463275683
1.3684-1.38510.18083750.117830793454100
1.3851-1.40260.16033740.103929903364100
1.4026-1.42110.15073520.101230763428100
1.4211-1.44050.15393350.099730923427100
1.4405-1.46110.14833330.098330383371100
1.4611-1.48290.13933380.093531043442100
1.4829-1.50610.14413400.091830593399100
1.5061-1.53080.14123640.087230303394100
1.5308-1.55720.12383340.083431223456100
1.5572-1.58550.12583510.078330283379100
1.5855-1.61590.11563220.079630973419100
1.6159-1.64890.12383400.077530823422100
1.6489-1.68480.12413360.082530663402100
1.6848-1.72390.12633470.081431123459100
1.7239-1.7670.12693420.084830853427100
1.767-1.81480.12983320.081630423374100
1.8148-1.86810.11243460.081131113457100
1.8681-1.92840.11223380.085330643402100
1.9284-1.99720.133320.086530913423100
1.9972-2.07710.11373800.090430473427100
2.0771-2.17150.1323530.088230743427100
2.1715-2.28590.12023500.085430593409100
2.2859-2.42890.11653280.092831393467100
2.4289-2.6160.12123420.095630803422100
2.616-2.87860.1383330.10431033436100
2.8786-3.29350.13483500.109130843434100
3.2935-4.14340.12673130.103831563469100
4.1434-19.97720.14183690.127331453514100

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