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- PDB-4zyo: Crystal Structure of Human Integral Membrane Stearoyl-CoA Desatur... -

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Basic information

Entry
Database: PDB / ID: 4zyo
TitleCrystal Structure of Human Integral Membrane Stearoyl-CoA Desaturase with Substrate
ComponentsAcyl-CoA desaturase
KeywordsOXIDOREDUCTASE / Membrane protein / Desaturase / Metal binding protein
Function / homology
Function and homology information


stearoyl-CoA 9-desaturase / stearoyl-CoA 9-desaturase activity / palmitoyl-CoA 9-desaturase activity / fatty-acyl-CoA biosynthetic process / unsaturated fatty acid biosynthetic process / regulation of cholesterol biosynthetic process / : / monounsaturated fatty acid biosynthetic process / Fatty acyl-CoA biosynthesis / NR1H2 & NR1H3 regulate gene expression linked to lipogenesis ...stearoyl-CoA 9-desaturase / stearoyl-CoA 9-desaturase activity / palmitoyl-CoA 9-desaturase activity / fatty-acyl-CoA biosynthetic process / unsaturated fatty acid biosynthetic process / regulation of cholesterol biosynthetic process / : / monounsaturated fatty acid biosynthetic process / Fatty acyl-CoA biosynthesis / NR1H2 & NR1H3 regulate gene expression linked to lipogenesis / response to fatty acid / Activation of gene expression by SREBF (SREBP) / positive regulation of cold-induced thermogenesis / membrane => GO:0016020 / oxidoreductase activity / iron ion binding / endoplasmic reticulum membrane / nucleolus / endoplasmic reticulum / membrane
Similarity search - Function
Fatty acid desaturase type 1, conserved site / Acyl-CoA desaturase / Fatty acid desaturases family 1 signature.
Similarity search - Domain/homology
STEAROYL-COENZYME A / Acyl-CoA desaturase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.25 Å
AuthorsWang, H. / Klein, M.G. / Lane, W. / Snell, G. / Levin, I. / Li, K. / Zou, H. / Sang, B.-C.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2015
Title: Crystal structure of human stearoyl-coenzyme A desaturase in complex with substrate.
Authors: Wang, H. / Klein, M.G. / Zou, H. / Lane, W. / Snell, G. / Levin, I. / Li, K. / Sang, B.C.
History
DepositionMay 21, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 17, 2015Provider: repository / Type: Initial release
Revision 1.1Jul 29, 2015Group: Database references
Revision 1.2Mar 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Experimental preparation / Source and taxonomy
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / entity_src_gen / exptl_crystal / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_src_gen.pdbx_alt_source_flag / _exptl_crystal.density_Matthews / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Acyl-CoA desaturase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,4745
Polymers36,7981
Non-polymers1,6754
Water181
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)134.108, 134.108, 112.561
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Acyl-CoA desaturase / Delta(9)-desaturase / Delta-9 desaturase / Fatty acid desaturase / Stearoyl-CoA desaturase


Mass: 36798.211 Da / Num. of mol.: 1 / Fragment: UNP residues 45-359 / Mutation: K60A, K62A, E63A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SCD / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: O00767, stearoyl-CoA 9-desaturase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-ST9 / STEAROYL-COENZYME A / Stearoyl-CoA


Mass: 1033.996 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C39H70N7O17P3S
#4: Sugar ChemComp-LMT / DODECYL-BETA-D-MALTOSIDE


Type: D-saccharide / Mass: 510.615 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H46O11 / Comment: detergent*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 7.94 Å3/Da
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: 100 mM Tris-HCl (pH 8.5), 30-35% (v/v) PEG400, 220 mM sodium citrate

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.113 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 14, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.113 Å / Relative weight: 1
ReflectionResolution: 3.25→116 Å / Num. obs: 18812 / % possible obs: 100 % / Redundancy: 20 % / Rmerge F obs: 0.118 / Net I/σ(I): 19

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 3.25→37.52 Å / SU ML: 0.54 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 29.43 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2636 966 5.14 %
Rwork0.2413 --
obs0.2424 18788 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.25→37.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2466 0 92 1 2559
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0042647
X-RAY DIFFRACTIONf_angle_d0.9413604
X-RAY DIFFRACTIONf_dihedral_angle_d14.862917
X-RAY DIFFRACTIONf_chiral_restr0.035376
X-RAY DIFFRACTIONf_plane_restr0.004435
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.25-3.42090.38191460.3392509X-RAY DIFFRACTION100
3.4209-3.63510.30451440.29232517X-RAY DIFFRACTION100
3.6351-3.91550.29331340.24792493X-RAY DIFFRACTION100
3.9155-4.3090.2821310.24132540X-RAY DIFFRACTION100
4.309-4.93140.26371390.22392532X-RAY DIFFRACTION100
4.9314-6.20840.25761360.24162571X-RAY DIFFRACTION100
6.2084-37.52280.23231360.22672660X-RAY DIFFRACTION100

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