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- PDB-6ohu: Structure of EBP and tamoxifen -

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Basic information

Entry
Database: PDB / ID: 6ohu
TitleStructure of EBP and tamoxifen
Components3-beta-hydroxysteroid-Delta(8),Delta(7)-isomerase
Keywordsmembrane protein / isomerase/inhibitor / Isomerase / isomerase-inhibitor complex
Function / homology
Function and homology information


cholestenol Delta-isomerase / C-8 sterol isomerase activity / cholesterol biosynthetic process via desmosterol / cholesterol biosynthetic process via lathosterol / cholestenol delta-isomerase activity / Cholesterol biosynthesis via desmosterol / Cholesterol biosynthesis via lathosterol / cholesterol-5,6-oxide hydrolase / cholesterol-5,6-oxide hydrolase activity / steroid Delta-isomerase activity ...cholestenol Delta-isomerase / C-8 sterol isomerase activity / cholesterol biosynthetic process via desmosterol / cholesterol biosynthetic process via lathosterol / cholestenol delta-isomerase activity / Cholesterol biosynthesis via desmosterol / Cholesterol biosynthesis via lathosterol / cholesterol-5,6-oxide hydrolase / cholesterol-5,6-oxide hydrolase activity / steroid Delta-isomerase activity / ossification involved in bone maturation / cholesterol biosynthetic process / hemopoiesis / cholesterol metabolic process / nuclear envelope / cytoplasmic vesicle / nuclear membrane / endoplasmic reticulum membrane / endoplasmic reticulum / identical protein binding
Similarity search - Function
Emopamil-binding protein / EXPERA domain / EXPERA (EXPanded EBP superfamily) / EXPERA domain profile.
Similarity search - Domain/homology
Chem-CTX / 3-beta-hydroxysteroid-Delta(8),Delta(7)-isomerase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.526 Å
AuthorsLong, T. / Li, X.
CitationJournal: Nat Commun / Year: 2019
Title: Structural basis for human sterol isomerase in cholesterol biosynthesis and multidrug recognition.
Authors: Long, T. / Hassan, A. / Thompson, B.M. / McDonald, J.G. / Wang, J. / Li, X.
History
DepositionApr 6, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 19, 2019Provider: repository / Type: Initial release
Revision 1.1Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: 3-beta-hydroxysteroid-Delta(8),Delta(7)-isomerase
B: 3-beta-hydroxysteroid-Delta(8),Delta(7)-isomerase
C: 3-beta-hydroxysteroid-Delta(8),Delta(7)-isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,3806
Polymers82,2663
Non-polymers1,1153
Water00
1
A: 3-beta-hydroxysteroid-Delta(8),Delta(7)-isomerase
B: 3-beta-hydroxysteroid-Delta(8),Delta(7)-isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,5874
Polymers54,8442
Non-polymers7432
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5100 Å2
ΔGint-37 kcal/mol
Surface area19590 Å2
MethodPISA
2
C: 3-beta-hydroxysteroid-Delta(8),Delta(7)-isomerase
hetero molecules

C: 3-beta-hydroxysteroid-Delta(8),Delta(7)-isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,5874
Polymers54,8442
Non-polymers7432
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-x,-y-1,z1
Buried area5150 Å2
ΔGint-35 kcal/mol
Surface area19690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)192.837, 66.829, 98.678
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein 3-beta-hydroxysteroid-Delta(8),Delta(7)-isomerase / Cholestenol Delta-isomerase / Delta(8)-Delta(7) sterol isomerase / D8-D7 sterol isomerase / ...Cholestenol Delta-isomerase / Delta(8)-Delta(7) sterol isomerase / D8-D7 sterol isomerase / Emopamil-binding protein / EBP


Mass: 27421.871 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EBP / Production host: Homo sapiens (human) / References: UniProt: Q15125, cholestenol Delta-isomerase
#2: Chemical ChemComp-CTX / (Z)-2-[4-(1,2)-DIPHENYL-1-BUTENYL)-PHENOXY]-N,N-DIMETHYLETHANAMINE / TRANS FORM OF TAMOXIFEN


Mass: 371.515 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C26H29NO

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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: 3.86 Å3/Da / Density % sol: 68.17 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / Details: Hepes, peg 600

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0,979
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 16, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
101
29791
ReflectionResolution: 3.5→50 Å / Num. obs: 13685 / % possible obs: 99.6 % / Redundancy: 6.3 % / CC1/2: 0.95 / Net I/σ(I): 17.3
Reflection shellResolution: 3.5→3.57 Å / Num. unique obs: 821 / CC1/2: 0.358

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 3.526→47.799 Å / SU ML: 0.51 / Cross valid method: NONE / σ(F): 1.35 / Phase error: 32.68
RfactorNum. reflection% reflection
Rfree0.3259 1369 10 %
Rwork0.2725 --
obs0.2778 13685 83.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.526→47.799 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5124 0 84 0 5208
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0045404
X-RAY DIFFRACTIONf_angle_d0.9277389
X-RAY DIFFRACTIONf_dihedral_angle_d9.6462931
X-RAY DIFFRACTIONf_chiral_restr0.048798
X-RAY DIFFRACTIONf_plane_restr0.006891
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.5263-3.65230.698120.299916X-RAY DIFFRACTION1
3.6523-3.79840.3422670.2907603X-RAY DIFFRACTION42
3.7984-3.97120.33751510.26551364X-RAY DIFFRACTION94
3.9712-4.18050.34771610.25081446X-RAY DIFFRACTION100
4.1805-4.44220.29011620.24451457X-RAY DIFFRACTION100
4.4422-4.78490.30351610.23921450X-RAY DIFFRACTION100
4.7849-5.26590.29151620.25711455X-RAY DIFFRACTION100
5.2659-6.02660.37061650.33121485X-RAY DIFFRACTION100
6.0266-7.5880.34681630.31811471X-RAY DIFFRACTION98
7.588-47.80360.33451750.30691569X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: -26.238 Å / Origin y: -4.127 Å / Origin z: 43.7791 Å
111213212223313233
T0.263 Å2-0.1505 Å20.3134 Å2-0.1856 Å20.1714 Å2--0.1185 Å2
L-0.0294 °20.0332 °20.5832 °2-0.1007 °2-0.959 °2--0.3898 °2
S-0.011 Å °-0.0765 Å °-0.1307 Å °-0.2933 Å °0.1066 Å °0.1958 Å °0.0375 Å °-0.189 Å °-0.0084 Å °
Refinement TLS groupSelection details: all

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