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- PDB-4u2t: Cholesterol oxidase in the oxidised state complexed with isopropanol -

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Basic information

Entry
Database: PDB / ID: 4u2t
TitleCholesterol oxidase in the oxidised state complexed with isopropanol
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
: / 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 / Twin arginine translocation (Tat) signal profile. / Twin-arginine translocation pathway, signal sequence / 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-ADENINE DINUCLEOTIDE / Cholesterol oxidase
Similarity search - Component
Biological speciesStreptomyces sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.223 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 18, 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)56,6803
Polymers55,7991
Non-polymers8822
Water6,900383
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)51.400, 73.970, 63.590
Angle α, β, γ (deg.)90.000, 105.370, 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) / Strain (production host): BL21(DE3)
References: UniProt: P12676, cholesterol oxidase, steroid Delta-isomerase
#2: Chemical ChemComp-SO4 / SULFATE ION


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


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


Mass: 18.015 Da / Num. of mol.: 383 / 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: 2.14 Å3/Da / Density % sol: 42.46 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: PEG 8000, manganese sulfate, cacodylate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9658 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Nov 26, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9658 Å / Relative weight: 1
ReflectionResolution: 1.223→61.316 Å / Num. all: 132630 / Num. obs: 132630 / % possible obs: 98.3 % / Redundancy: 4 % / Biso Wilson estimate: 10.1 Å2 / Rpim(I) all: 0.042 / Rrim(I) all: 0.086 / Rsym value: 0.074 / Net I/av σ(I): 7.207 / Net I/σ(I): 10.3 / Num. measured all: 526499
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRsym valueNet I/σ(I) obs% possible all
1.223-1.293.90.6741.172894189090.3910.674296.4
1.29-1.373.90.51.470452179980.2880.52.897.1
1.37-1.463.90.3542.166927171170.2040.3543.897.9
1.46-1.583.90.2253.362582159880.130.2255.998.5
1.58-1.7340.1445.258706148310.0820.1448.498.9
1.73-1.934.10.0927.654651134910.0520.09212.799.4
1.93-2.234.10.0611.349320119570.0340.0618.599.8
2.23-2.734.10.05110.741892101570.0290.05123.299.9
2.73-3.874.10.03616.43231478710.020.03629100
3.87-19.2143.90.03317.41676143110.0190.03331.398.2

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.9_1692)refinement
SCALA3.3.21data scaling
PDB_EXTRACT3.14data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1MXT

1mxt


Resolution: 1.223→19.214 Å / SU ML: 0.11 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 14.08 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.149 6682 5.04 %
Rwork0.119 125889 -
obs0.1205 132571 98.16 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 112.16 Å2 / Biso mean: 15.4351 Å2 / Biso min: 5.93 Å2
Refinement stepCycle: final / Resolution: 1.223→19.214 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3817 0 89 404 4310
Biso mean--8.85 28.95 -
Num. residues----498
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.014333
X-RAY DIFFRACTIONf_angle_d1.4515968
X-RAY DIFFRACTIONf_chiral_restr0.086638
X-RAY DIFFRACTIONf_plane_restr0.008801
X-RAY DIFFRACTIONf_dihedral_angle_d13.181573
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 (%)
1.223-1.23690.27582170.25514034425196
1.2369-1.25140.28872020.23354131433395
1.2514-1.26670.27352120.23044084429697
1.2667-1.28270.24652190.20154098431797
1.2827-1.29960.24432260.20924111433796
1.2996-1.31740.22442200.18444101432197
1.3174-1.33620.20252260.17114120434697
1.3362-1.35620.19032200.16264158437897
1.3562-1.37730.21152170.16824131434897
1.3773-1.39990.21872280.14764142437098
1.3999-1.42410.18282080.13124186439497
1.4241-1.44990.1732110.13784163437498
1.4499-1.47780.18362260.12784220444698
1.4778-1.5080.16322130.11494168438198
1.508-1.54070.15632340.11454145437998
1.5407-1.57660.14522040.09414257446198
1.5766-1.6160.12762140.08764191440598
1.616-1.65960.1252220.08474236445899
1.6596-1.70850.11612020.08474259446199
1.7085-1.76360.11862400.08254238447899
1.7636-1.82660.11662460.08134170441699
1.8266-1.89960.11792450.08574238448399
1.8996-1.9860.12042140.09454281449599
1.986-2.09060.12022450.088542274472100
2.0906-2.22140.10582460.082242744520100
2.2214-2.39260.1242380.098842484486100
2.3926-2.63280.12172160.092343294545100
2.6328-3.01260.12722340.100442904524100
3.0126-3.79070.13452160.11243144530100
3.7907-19.2160.18632210.16974345456699

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