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- PDB-4xxg: Structure of protonated Cholesterol Oxidase from Streptomyces SA-COO -

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Basic information

Entry
Database: PDB / ID: 4xxg
TitleStructure of protonated Cholesterol Oxidase from Streptomyces SA-COO
ComponentsCholesterol oxidase
KeywordsOXIDOREDUCTASE
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. SA-COO (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.85 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 30, 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_radiation_wavelength / 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)56,5842
Polymers55,7991
Non-polymers7861
Water12,268681
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)51.299, 72.761, 63.030
Angle α, β, γ (deg.)90.000, 105.130, 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 681 / 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: 40.94 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / 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: 0.82472 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: 0.82472 Å / Relative weight: 1
ReflectionResolution: 0.85→60.846 Å / Num. all: 390495 / Num. obs: 390495 / % possible obs: 100 % / Redundancy: 14.4 % / Biso Wilson estimate: 6.39 Å2 / Rpim(I) all: 0.028 / Rrim(I) all: 0.127 / Rsym value: 0.124 / Net I/av σ(I): 2.506 / Net I/σ(I): 16.2 / Num. measured all: 5617181
Reflection shell

Diffraction-ID: 1 / Rejects: _ / % possible all: 100

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRsym valueNet I/σ(I) obs
0.85-0.980.9770.8457672568900.3620.9772.5
0.9-0.958.20.5571.3439309538680.2050.5574.1
0.95-1.028.30.3172.4417846506110.1160.3176.5
1.02-1.112.70.6310.9600466471650.180.63110.8
1.1-1.213.30.3461.7576991433900.0980.34616
1.2-1.3415.90.2912.1625453392600.0740.29119.5
1.34-1.5522.80.2183.1791221346900.0460.21825
1.55-1.926.40.1155.9773186293110.0230.11535.6
1.9-2.6926.50.078.6602875227290.0140.0746.4
2.69-44.51526.40.0955332162125810.0190.09555.4

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Processing

Software
NameClassification
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1MXT

1mxt


Resolution: 0.85→34.278 Å / SU ML: 0.05 / Cross valid method: THROUGHOUT / σ(F): 0.01 / Phase error: 11.46 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1239 38369 4.96 %RANDOM
Rwork0.1133 735662 --
obs0.1138 774031 99.97 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 171.54 Å2 / Biso mean: 10.9052 Å2 / Biso min: 2.67 Å2
Refinement stepCycle: final / Resolution: 0.85→34.278 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3834 0 84 745 4663
Biso mean--4.16 22.64 -
Num. residues----499
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0094420
X-RAY DIFFRACTIONf_angle_d1.5296082
X-RAY DIFFRACTIONf_chiral_restr0.093646
X-RAY DIFFRACTIONf_plane_restr0.009815
X-RAY DIFFRACTIONf_dihedral_angle_d13.2141620
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
0.8501-0.85980.255912650.25092434725612
0.8598-0.86990.248112710.23512454525816
0.8699-0.88050.232312520.22422451725769
0.8805-0.89160.212212940.21172456725861
0.8916-0.90340.210612880.1992450125789
0.9034-0.91570.201412550.18562456025815
0.9157-0.92880.186213090.17172451025819
0.9288-0.94270.16612490.15862455425803
0.9427-0.95740.156912630.15042456525828
0.9574-0.97310.149713150.13662444025755
0.9731-0.98990.141913040.1282453225836
0.9899-1.00790.126912530.11792454625799
1.0079-1.02730.124113160.10892446325779
1.0273-1.04820.107312640.10342460425868
1.0482-1.0710.105312600.09612461025870
1.071-1.0960.107913180.08852440425722
1.096-1.12340.102213970.08522444025837
1.1234-1.15370.090812290.08262458325812
1.1537-1.18770.094912760.0832458925865
1.1877-1.2260.093512600.0862440825668
1.226-1.26990.094412930.08672452525818
1.2699-1.32070.098113210.08712453625857
1.3207-1.38080.098613580.08752440325761
1.3808-1.45360.10112400.0892457225812
1.4536-1.54470.101612580.08912453925797
1.5447-1.66390.109713400.0932451625856
1.6639-1.83140.111712230.09962458325806
1.8314-2.09640.113512540.11032452225776
2.0964-2.6410.122612620.1132454825810
2.641-34.30590.138711820.12572463325815

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