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- PDB-4xwr: X-ray structure of perdeuterated Cholesterol Oxidase from Strepto... -

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Basic information

Entry
Database: PDB / ID: 4xwr
TitleX-ray structure of perdeuterated Cholesterol Oxidase from Streptomyces SA-COO
ComponentsCholesterol oxidase
KeywordsOXIDOREDUCTASE / perdeuteration
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. SA-COO (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.1 Å
AuthorsGolden, E. / Vrielink, A.
CitationJournal: Anal.Biochem. / Year: 2015
Title: Production and characterization of recombinant perdeuterated cholesterol oxidase.
Authors: Golden, E. / Attwood, P.V. / Duff, A.P. / Meilleur, F. / Vrielink, A.
History
DepositionJan 29, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 30, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 27, 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 / diffrn_source / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation

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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
Water12,178676
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1630 Å2
ΔGint-24 kcal/mol
Surface area17950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.227, 73.102, 63.171
Angle α, β, γ (deg.)90.000, 105.140, 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. SA-COO (bacteria) / Gene: choA / Production host: Escherichia coli (E. coli)
References: UniProt: P12676, cholesterol oxidase, steroid Delta-isomerase
#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: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 676 / 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: 2.09 Å3/Da / Density % sol: 41.26 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.2 / Details: PEG 8K, MnSO4, sodium cacodylate

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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: Jun 10, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.1→60.98 Å / Num. all: 178806 / Num. obs: 178806 / % possible obs: 98.4 % / Redundancy: 10.7 % / Biso Wilson estimate: 5.87 Å2 / Rpim(I) all: 0.022 / Rrim(I) all: 0.08 / Rsym value: 0.077 / Net I/av σ(I): 4.307 / Net I/σ(I): 20.3 / Num. measured all: 1910430
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
1.1-1.167.30.2542.9187345255310.10.2547.896.4
1.16-1.237.40.1963.8179377243280.0770.1969.697.2
1.23-1.317.40.1624.6170283230450.0640.16211.197.8
1.31-1.427.40.1285.7159578215460.050.12813.298.3
1.42-1.5612.30.1365.2245604199660.0390.13618.598.8
1.56-1.7414.90.0997270981181490.0260.09925.399.4
1.74-2.0114.90.0699.1239274160900.0190.06932.599.8
2.01-2.4615.20.05710.4207110136670.0150.05740100
2.46-3.4815.20.0588.7161588105960.0150.05844.8100
3.48-46.82715.20.076.68929058880.0180.0748.6100

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Processing

Software
NameVersionClassification
PHENIXrefinement
SCALA3.3.21data scaling
PDB_EXTRACT3.15data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1MXT

1mxt


Resolution: 1.1→40.959 Å / SU ML: 0.05 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 7.13 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1072 8967 5.02 %
Rwork0.0931 169810 -
obs0.0939 178777 98.38 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 73.39 Å2 / Biso mean: 9.3747 Å2 / Biso min: 2.1 Å2
Refinement stepCycle: final / Resolution: 1.1→40.959 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3834 0 89 736 4659
Biso mean--3.92 20.45 -
Num. residues----499
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0114420
X-RAY DIFFRACTIONf_angle_d1.5656082
X-RAY DIFFRACTIONf_chiral_restr0.101646
X-RAY DIFFRACTIONf_plane_restr0.01815
X-RAY DIFFRACTIONf_dihedral_angle_d13.0051620
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 (%)
1.1-1.11250.12152700.09285594586496
1.1125-1.12560.1042600.08625503576396
1.1256-1.13930.10962830.08445565584897
1.1393-1.15370.10653130.07885500581397
1.1537-1.16890.10083080.07555533584197
1.1689-1.18490.08693190.07435529584897
1.1849-1.20190.12830.07715566584997
1.2019-1.21980.09342880.07625642593097
1.2198-1.23890.0993000.07725565586597
1.2389-1.25920.09093200.07375578589898
1.2592-1.28090.09563050.07435604590998
1.2809-1.30420.09563060.07875583588998
1.3042-1.32930.10223160.07575609592598
1.3293-1.35640.10132830.0755670595398
1.3564-1.38590.09893300.07455637596798
1.3859-1.41810.1052870.07655644593199
1.4181-1.45360.0982930.07595648594199
1.4536-1.49290.09413100.07355701601199
1.4929-1.53680.09952900.07355718600899
1.5368-1.58650.09272750.07365714598999
1.5865-1.64320.09592840.07655709599399
1.6432-1.70890.10363050.08255757606299
1.7089-1.78670.10212900.086357336023100
1.7867-1.88090.10472920.09257306022100
1.8809-1.99880.10633020.094557616063100
1.9988-2.15310.10593160.096957656081100
2.1531-2.36970.11283150.102957536068100
2.3697-2.71260.11893120.112658126124100
2.7126-3.41730.12293150.119357936108100
3.4173-40.98760.12092970.12358946191100

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