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- PDB-4zr0: Full length scs7p (only hydroxylase domain visible) -

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Basic information

Entry
Database: PDB / ID: 4zr0
TitleFull length scs7p (only hydroxylase domain visible)
ComponentsCeramide very long chain fatty acid hydroxylase SCS7
KeywordsOXIDOREDUCTASE / fatty acid hydroxylase / scs7p / fah1p / fa2h / Structural Genomics / PSI-Biology / Membrane Protein Structural Biology Consortium / MPSBC
Function / homology
Function and homology information


4-hydroxysphinganine ceramide fatty acyl 2-hydroxylase / dihydroceramide fatty acyl 2-hydroxylase / inositol phosphoceramide metabolic process / dihydroceramide fatty acyl 2-hydroxylase activity / fatty acid 2-hydroxylase activity / Sphingolipid de novo biosynthesis / ceramide biosynthetic process / fatty acid metabolic process / fatty acid biosynthetic process / iron ion binding ...4-hydroxysphinganine ceramide fatty acyl 2-hydroxylase / dihydroceramide fatty acyl 2-hydroxylase / inositol phosphoceramide metabolic process / dihydroceramide fatty acyl 2-hydroxylase activity / fatty acid 2-hydroxylase activity / Sphingolipid de novo biosynthesis / ceramide biosynthetic process / fatty acid metabolic process / fatty acid biosynthetic process / iron ion binding / heme binding / endoplasmic reticulum membrane / endoplasmic reticulum / zinc ion binding
Similarity search - Function
Fatty acid hydroxylase / Sterol desaturase Scs7 / Fatty acid hydroxylase / Cytochrome b5, heme-binding site / Cytochrome b5 family, heme-binding domain signature. / Cytochrome b5 family, heme-binding domain profile. / Cytochrome b5-like heme/steroid binding domain / Cytochrome b5-like heme/steroid binding domain superfamily / Cytochrome b5-like Heme/Steroid binding domain / Cytochrome b5-like Heme/Steroid binding domain
Similarity search - Domain/homology
Ceramide very long chain fatty acid hydroxylase SCS7
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 3.8 Å
AuthorsZhu, G. / Koszelak-Rosenblum, M. / Malkowski, M.G. / Membrane Protein Structural Biology Consortium (MPSBC)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)U54 GM094611 United States
CitationJournal: J.Biol.Chem. / Year: 2015
Title: The Crystal Structure of an Integral Membrane Fatty Acid alpha-Hydroxylase.
Authors: Zhu, G. / Koszelak-Rosenblum, M. / Connelly, S.M. / Dumont, M.E. / Malkowski, M.G.
History
DepositionMay 11, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 29, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 18, 2015Group: Database references
Revision 1.2Dec 23, 2015Group: Database references
Revision 1.3Sep 6, 2017Group: Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Mar 6, 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: Ceramide very long chain fatty acid hydroxylase SCS7
B: Ceramide very long chain fatty acid hydroxylase SCS7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,8886
Polymers91,6272
Non-polymers2624
Water00
1
A: Ceramide very long chain fatty acid hydroxylase SCS7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,9443
Polymers45,8131
Non-polymers1312
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Ceramide very long chain fatty acid hydroxylase SCS7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,9443
Polymers45,8131
Non-polymers1312
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)202.943, 202.943, 202.943
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number199
Space group name H-MI213

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Components

#1: Protein Ceramide very long chain fatty acid hydroxylase SCS7 / Ceramide VLCFA hydroxylase SCS7 / Suppressor of calcium sensitivity 7


Mass: 45813.316 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: SCS7, FAH1, YMR272C, YM8156.14C / Plasmid: pSGP46 / Production host: Saccharomyces cerevisiae (brewer's yeast) / Strain (production host): BJ5460 / References: UniProt: Q03529, Oxidoreductases
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.8 Å3/Da / Density % sol: 67.64 %
Crystal growTemperature: 287 K / Method: batch mode / pH: 7 / Details: 20% PEG3350, 0.1M Hepes, pH7.0, 0.3M (NH4)2SO4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1.74 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Oct 21, 2012
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.74 Å / Relative weight: 1
ReflectionResolution: 3.8→50 Å / Num. all: 15028 / Num. obs: 15000 / % possible obs: 99.5 % / Redundancy: 4.4 % / Rmerge(I) obs: 0.122 / Net I/σ(I): 8.5
Reflection shellResolution: 3.8→3.94 Å / Redundancy: 4.3 % / Rmerge(I) obs: 1.592 / Mean I/σ(I) obs: 1.1 / % possible all: 99.7

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Processing

Software
NameVersionClassification
PHENIX1.8.2_1309refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: SIRAS / Resolution: 3.8→47.834 Å / SU ML: 0.58 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 30.97 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2707 699 5.05 %Random selection
Rwork0.2461 ---
obs0.2473 13852 99.85 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.8→47.834 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4466 0 4 0 4470
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0034649
X-RAY DIFFRACTIONf_angle_d0.7236325
X-RAY DIFFRACTIONf_dihedral_angle_d10.5411615
X-RAY DIFFRACTIONf_chiral_restr0.03644
X-RAY DIFFRACTIONf_plane_restr0.004782
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.8001-4.09340.38551530.33752596X-RAY DIFFRACTION100
4.0934-4.50510.30321360.25842615X-RAY DIFFRACTION100
4.5051-5.15630.24781270.21142622X-RAY DIFFRACTION100
5.1563-6.49380.25941530.24932614X-RAY DIFFRACTION100
6.4938-47.83790.24491300.23772706X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.182-0.0480.11010.0498-0.0079-0.13380.01070.1286-0.32570.1935-0.019-0.00630.2319-0.07570.3295-0.3170.08140.37850.3266-0.09890.258176.732543.5127126.5587
20.56660.1878-0.25140.28180.05270.2152-0.19790.75860.716-0.08510.3638-0.091-0.1859-0.011-0.16050.12320.03420.21620.64610.08090.386963.36975.7401124.7643
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 117 through 380 )
2X-RAY DIFFRACTION2chain 'B' and (resid 119 through 388 )

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