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- PDB-4rek: Crystal structure and charge density studies of cholesterol oxida... -

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Basic information

Entry
Database: PDB / ID: 4rek
TitleCrystal structure and charge density studies of cholesterol oxidase from Brevibacterium sterolicum at 0.74 ultra-high resolution
ComponentsCholesterol oxidase
KeywordsOXIDOREDUCTASE / Oxidase / FAD Binding / Membrane
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
FLAVIN-ADENINE DINUCLEOTIDE / PHOSPHATE ION / Cholesterol oxidase
Similarity search - Component
Biological speciesStreptomyces sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.74 Å
AuthorsZarychta, B. / Lyubimov, A. / Ahmed, M. / Munshi, P. / Guillot, B. / Vrielink, A.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2015
Title: Cholesterol oxidase: ultrahigh-resolution crystal structure and multipolar atom model-based analysis.
Authors: Zarychta, B. / Lyubimov, A. / Ahmed, M. / Munshi, P. / Guillot, B. / Vrielink, A. / Jelsch, C.
History
DepositionSep 23, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 15, 2015Provider: repository / Type: Initial release
Revision 1.1Jun 3, 2015Group: Database references
Revision 1.2Nov 22, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Sep 20, 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 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)55,4063
Polymers54,5251
Non-polymers8812
Water16,159897
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)51.240, 72.920, 63.010
Angle α, β, γ (deg.)90.00, 105.13, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 54525.277 Da / Num. of mol.: 1 / Fragment: UNP residues 64-544
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)
References: UniProt: P12676, cholesterol oxidase, steroid Delta-isomerase
#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE / Flavin adenine dinucleotide


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 897 / 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: 5

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Sample preparation

CrystalDensity Matthews: 2.08 Å3/Da / Density % sol: 40.98 %
Crystal growTemperature: 290.15 K / Method: vapor diffusion, hanging drop / pH: 5.2
Details: The crystallization solution was composed of 9-11% poly(ethylene glycol) (PEG) MW 8000, 75mM MnSO4 and 100mM sodium cacodylate buffer., pH 5.2, VAPOR DIFFUSION, HANGING DROP, temperature 290.15K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.828 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD
RadiationScattering type: x-ray
Radiation wavelengthWavelength: 0.828 Å / Relative weight: 1
ReflectionResolution: 0.74→44.477 Å / Num. all: 465329 / Num. obs: 465329 / % possible obs: 78.78 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0

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Processing

Software
NameVersionClassification
Blu-IceIcedata collection
PHENIX(phenix.refine: 1.8.2_1309)refinement
d*TREKdata reduction
CCP4data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1N4U

1n4u


Resolution: 0.74→44.477 Å / SU ML: 0.06 / σ(F): 1.34 / Phase error: 14.91 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1231 23391 5.03 %RANDOM
Rwork0.1127 ---
all0.1132 465329 --
obs0.1132 465329 78.78 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 0.74→44.477 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3834 0 58 897 4789
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.014425
X-RAY DIFFRACTIONf_angle_d1.56086
X-RAY DIFFRACTIONf_dihedral_angle_d13.1731666
X-RAY DIFFRACTIONf_chiral_restr0.09670
X-RAY DIFFRACTIONf_plane_restr0.01794
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
0.7405-0.74890.5356440.49892X-RAY DIFFRACTION5
0.7489-0.75770.3562960.37272162X-RAY DIFFRACTION12
0.7577-0.76690.31451320.32412650X-RAY DIFFRACTION14
0.7669-0.77670.31861400.31732841X-RAY DIFFRACTION15
0.7767-0.78690.28832520.285036X-RAY DIFFRACTION27
0.7869-0.79770.30943600.27626695X-RAY DIFFRACTION36
0.7977-0.80910.27775130.26278758X-RAY DIFFRACTION47
0.8091-0.82110.26676260.25111235X-RAY DIFFRACTION61
0.8211-0.8340.24337010.23214005X-RAY DIFFRACTION75
0.834-0.84760.22758270.218615803X-RAY DIFFRACTION85
0.8476-0.86230.22899740.203417474X-RAY DIFFRACTION94
0.8623-0.87790.19299530.18218519X-RAY DIFFRACTION99
0.8779-0.89480.17349620.169918506X-RAY DIFFRACTION99
0.8948-0.91310.15829310.155618731X-RAY DIFFRACTION100
0.9131-0.93290.15619820.14918686X-RAY DIFFRACTION100
0.9329-0.95460.148510050.139718639X-RAY DIFFRACTION100
0.9546-0.97850.138610240.125318606X-RAY DIFFRACTION100
0.9785-1.0050.117510180.114518684X-RAY DIFFRACTION100
1.005-1.03460.11799840.109618685X-RAY DIFFRACTION100
1.0346-1.06790.11569840.100218697X-RAY DIFFRACTION100
1.0679-1.10610.103410040.09118667X-RAY DIFFRACTION100
1.1061-1.15040.09069910.088218710X-RAY DIFFRACTION100
1.1504-1.20280.092110230.085618654X-RAY DIFFRACTION100
1.2028-1.26620.10319380.094418524X-RAY DIFFRACTION99
1.2662-1.34550.10810350.095218520X-RAY DIFFRACTION99
1.3455-1.44940.11139570.095718589X-RAY DIFFRACTION99
1.4494-1.59530.10619760.09518747X-RAY DIFFRACTION100
1.5953-1.82610.11069780.100718742X-RAY DIFFRACTION100
1.8261-2.30070.11019590.100418802X-RAY DIFFRACTION100
2.3007-44.55780.134810220.123818679X-RAY DIFFRACTION98

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