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- PDB-6c6r: Human Squalene Epoxidase (SQLE, Squalene Monooxygenase) structure... -

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Basic information

Entry
Database: PDB / ID: 6c6r
TitleHuman Squalene Epoxidase (SQLE, Squalene Monooxygenase) structure with FAD
ComponentsSqualene monooxygenase
KeywordsOXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR / Cholesterol Synthesis Pathway / SQLE / ERG1 / FAD-dependent Monooxygenase / Complex / FLAVOPROTEIN / OXIDOREDUCTASE-OXIDOREDUCTASE INHIBITOR complex
Function / homology
Function and homology information


squalene monooxygenase / squalene monooxygenase activity / lipid droplet formation / sterol biosynthetic process / Cholesterol biosynthesis / cholesterol metabolic process / FAD binding / Activation of gene expression by SREBF (SREBP) / regulation of cell population proliferation / intracellular membrane-bounded organelle ...squalene monooxygenase / squalene monooxygenase activity / lipid droplet formation / sterol biosynthetic process / Cholesterol biosynthesis / cholesterol metabolic process / FAD binding / Activation of gene expression by SREBF (SREBP) / regulation of cell population proliferation / intracellular membrane-bounded organelle / endoplasmic reticulum membrane / endoplasmic reticulum / membrane
Similarity search - Function
Squalene epoxidase / Squalene monooxygenase / Squalene epoxidase / NAD(P)-binding Rossmann-like domain / FAD/NAD(P)-binding domain superfamily
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / DI(HYDROXYETHYL)ETHER / Squalene monooxygenase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsPadyana, A.K. / Jin, L.
Citation
Journal: Nat Commun / Year: 2019
Title: Structure and inhibition mechanism of the catalytic domain of human squalene epoxidase.
Authors: Padyana, A.K. / Gross, S. / Jin, L. / Cianchetta, G. / Narayanaswamy, R. / Wang, F. / Wang, R. / Fang, C. / Lv, X. / Biller, S.A. / Dang, L. / Mahoney, C.E. / Nagaraja, N. / Pirman, D. / ...Authors: Padyana, A.K. / Gross, S. / Jin, L. / Cianchetta, G. / Narayanaswamy, R. / Wang, F. / Wang, R. / Fang, C. / Lv, X. / Biller, S.A. / Dang, L. / Mahoney, C.E. / Nagaraja, N. / Pirman, D. / Sui, Z. / Popovici-Muller, J. / Smolen, G.A.
#1: Journal: Nat Commun / Year: 2019
Title: A chemical biology screen identifies a vulnerability of neuroendocrine cancer cells to SQLE inhibition.
Authors: Mahoney, C.E. / Pirman, D. / Chubukov, V. / Sleger, T. / Hayes, S. / Fan, Z.P. / Allen, E.L. / Chen, Y. / Huang, L. / Liu, M. / Zhang, Y. / McDonald, G. / Narayanaswamy, R. / Choe, S. / ...Authors: Mahoney, C.E. / Pirman, D. / Chubukov, V. / Sleger, T. / Hayes, S. / Fan, Z.P. / Allen, E.L. / Chen, Y. / Huang, L. / Liu, M. / Zhang, Y. / McDonald, G. / Narayanaswamy, R. / Choe, S. / Chen, Y. / Gross, S. / Cianchetta, G. / Padyana, A.K. / Murray, S. / Liu, W. / Marks, K.M. / Murtie, J. / Dorsch, M. / Jin, S. / Nagaraja, N. / Biller, S.A. / Roddy, T. / Popovici-Muller, J. / Smolen, G.A.
History
DepositionJan 19, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 16, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 23, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Mar 13, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.year / _citation_author.identifier_ORCID / _citation_author.name / _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: Squalene monooxygenase
B: Squalene monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,87913
Polymers101,7922
Non-polymers6,08711
Water1,04558
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10460 Å2
ΔGint-50 kcal/mol
Surface area35480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)126.390, 126.390, 166.010
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Squalene monooxygenase / Squalene epoxidase / SE


Mass: 50895.770 Da / Num. of mol.: 2 / Fragment: residues 118-574
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SQLE, ERG1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q14534, squalene monooxygenase
#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Chemical
ChemComp-CPS / 3-[(3-CHOLAMIDOPROPYL)DIMETHYLAMMONIO]-1-PROPANESULFONATE / CHAPS


Mass: 614.877 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C32H58N2O7S / Comment: detergent*YM
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 58 / 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: 3.81 Å3/Da / Density % sol: 67.74 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 0.2 M Ammonium sulfate, 0.1 M tri-Sodium citrate pH 5.6, 15 %(w/v) PEG 4000, 0.02 M Hexammine cobalt(III) chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 2, 2016
RadiationMonochromator: Cryo-cooled double flat crystal Si(III) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 3→109.457 Å / Num. all: 31176 / Num. obs: 31176 / % possible obs: 99.8 % / Redundancy: 7.4 % / Rpim(I) all: 0.047 / Rrim(I) all: 0.133 / Rsym value: 0.124 / Net I/av σ(I): 5.2 / Net I/σ(I): 10.6 / Num. measured all: 230183
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsRpim(I) allRrim(I) allRsym value% possible all
3-3.166.10.6881.144710.2910.750.68899.2
3.16-3.356.30.4231.842030.1780.460.42399.8
3.35-3.596.70.2632.840350.1080.2850.26399.9
3.59-3.877.30.1823.937420.0720.1960.182100
3.87-4.2480.1394.934690.0520.1490.139100
4.24-4.748.30.1165.731500.0430.1230.116100
4.74-5.4880.0966.627850.0360.1020.09699.8
5.48-6.718.50.1046.123830.0370.110.104100
6.71-9.4990.069.418720.0210.0640.06100
9.49-38.9128.50.04411.910660.0160.0470.04498.1

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575)refinement
SCALA3.3.21data scaling
PDB_EXTRACT3.24data extraction
MOSFLMdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3→38.912 Å / SU ML: 0.34 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 24.68 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2486 1534 4.93 %RANDOM
Rwork0.1902 ---
obs0.193 31145 99.68 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3→38.912 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7060 0 315 58 7433
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0047570
X-RAY DIFFRACTIONf_angle_d0.67710318
X-RAY DIFFRACTIONf_dihedral_angle_d9.844551
X-RAY DIFFRACTIONf_chiral_restr0.0461186
X-RAY DIFFRACTIONf_plane_restr0.0051259
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.0002-3.0970.34121310.27892619X-RAY DIFFRACTION99
3.097-3.20760.3551300.27882673X-RAY DIFFRACTION100
3.2076-3.3360.30181660.25492615X-RAY DIFFRACTION100
3.336-3.48770.31400.23552662X-RAY DIFFRACTION100
3.4877-3.67140.27391480.2112662X-RAY DIFFRACTION100
3.6714-3.90130.2791120.20072699X-RAY DIFFRACTION100
3.9013-4.20220.25181270.17732708X-RAY DIFFRACTION100
4.2022-4.62440.20981830.15922642X-RAY DIFFRACTION100
4.6244-5.29220.21131260.15592725X-RAY DIFFRACTION100
5.2922-6.66210.22461360.18142740X-RAY DIFFRACTION100
6.6621-38.91540.21211350.16422866X-RAY DIFFRACTION100

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