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- PDB-6oht: Structure of EBP and U18666A -

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Basic information

Entry
Database: PDB / ID: 6oht
TitleStructure of EBP and U18666A
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
3beta-(2-Diethylaminoethoxy)androst-5-en-17-one / 3-beta-hydroxysteroid-Delta(8),Delta(7)-isomerase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.2 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 1.1Nov 13, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)83,8506
Polymers82,6883
Non-polymers1,1633
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)55,9004
Polymers55,1252
Non-polymers7752
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3220 Å2
ΔGint-33 kcal/mol
Surface area20150 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)55,9004
Polymers55,1252
Non-polymers7752
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-x,-y-1,z1
Buried area3250 Å2
ΔGint-31 kcal/mol
Surface area20000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)194.566, 67.823, 96.858
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


Mass: 27562.555 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-MKM / 3beta-(2-Diethylaminoethoxy)androst-5-en-17-one


Mass: 387.599 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C25H41NO2
Has protein modificationY

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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: 3.88 Å3/Da / Density % sol: 68.33 %
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 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 16, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 3.2→50 Å / Num. obs: 28389 / % possible obs: 99.8 % / Redundancy: 12.9 % / CC1/2: 0.99 / Net I/σ(I): 30
Reflection shellResolution: 3.1382→3.26 Å / Num. unique obs: 2273 / CC1/2: 0.739

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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: 3.2→48.642 Å / SU ML: 0.36 / Cross valid method: NONE / σ(F): 1.34 / Phase error: 30.84
RfactorNum. reflection% reflection
Rfree0.3191 2842 10.01 %
Rwork0.2685 --
obs0.2735 28389 65.52 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.2→48.642 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5124 0 84 0 5208
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0045406
X-RAY DIFFRACTIONf_angle_d0.9277413
X-RAY DIFFRACTIONf_dihedral_angle_d10.712955
X-RAY DIFFRACTIONf_chiral_restr0.047813
X-RAY DIFFRACTIONf_plane_restr0.006885
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1382-3.19230.011220.457711X-RAY DIFFRACTION1
3.1923-3.25030.560360.396759X-RAY DIFFRACTION3
3.2503-3.31280.4968150.3222142X-RAY DIFFRACTION7
3.3128-3.38040.4259290.333260X-RAY DIFFRACTION13
3.3804-3.45390.4286430.3581363X-RAY DIFFRACTION19
3.4539-3.53420.4011670.324608X-RAY DIFFRACTION31
3.5342-3.62260.4739950.3215870X-RAY DIFFRACTION45
3.6226-3.72050.39561260.32251167X-RAY DIFFRACTION58
3.7205-3.82990.33471410.27781259X-RAY DIFFRACTION66
3.8299-3.95350.32751780.2581578X-RAY DIFFRACTION80
3.9535-4.09470.29961970.25581766X-RAY DIFFRACTION92
4.0947-4.25860.33812110.24641938X-RAY DIFFRACTION98
4.2586-4.45230.29422110.23321947X-RAY DIFFRACTION100
4.4523-4.68680.29662140.21871922X-RAY DIFFRACTION100
4.6868-4.98020.26932140.2331944X-RAY DIFFRACTION100
4.9802-5.36430.33242140.26851978X-RAY DIFFRACTION100
5.3643-5.90330.3262160.30941935X-RAY DIFFRACTION100
5.9033-6.75550.32882190.32841954X-RAY DIFFRACTION100
6.7555-8.50380.29762270.26581932X-RAY DIFFRACTION99
8.5038-48.64730.27582170.28011914X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: -26.5989 Å / Origin y: -4.861 Å / Origin z: 43.3307 Å
111213212223313233
T0.0786 Å2-0.1087 Å20.003 Å2-0.0656 Å20.0396 Å2--0.0356 Å2
L0.0048 °20.0197 °20.0095 °2-0.0016 °2-0.0362 °2--0.0072 °2
S-0.0472 Å °-0.0045 Å °-0.0125 Å °-0.0443 Å °0.0351 Å °-0.0002 Å °-0.0034 Å °0.0397 Å °-0.0197 Å °
Refinement TLS groupSelection details: all

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