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- PDB-4zr1: Hydroxylase domain of scs7p -

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Basic information

Entry
Database: PDB / ID: 4zr1
TitleHydroxylase domain of scs7p
ComponentsCeramide very long chain fatty acid hydroxylase SCS7
KeywordsOXIDOREDUCTASE / fatty acid hydroxylase / scs7p / fah1p / fa2h homolog / 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 / 4-hydroxysphinganine ceramide fatty acyl 2-hydroxylase activity / fatty acid 2-hydroxylase activity / Sphingolipid de novo biosynthesis / very long-chain fatty acid metabolic process / ceramide biosynthetic process ...4-hydroxysphinganine ceramide fatty acyl 2-hydroxylase / dihydroceramide fatty acyl 2-hydroxylase / : / inositol phosphoceramide metabolic process / dihydroceramide fatty acyl 2-hydroxylase activity / 4-hydroxysphinganine ceramide fatty acyl 2-hydroxylase activity / fatty acid 2-hydroxylase activity / Sphingolipid de novo biosynthesis / very long-chain fatty acid metabolic process / ceramide biosynthetic process / fatty acid metabolic process / fatty acid biosynthetic process / iron ion binding / heme binding / endoplasmic reticulum membrane / endoplasmic reticulum / zinc ion binding / membrane
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
TRIDECANE / Ceramide very long chain fatty acid hydroxylase SCS7
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.6008 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 1.5Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _chem_comp.mon_nstd_flag / _chem_comp.name ..._chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.6Mar 6, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
Item: _chem_comp.pdbx_synonyms / _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: 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)74,15322
Polymers70,0782
Non-polymers4,07520
Water00
1
A: Ceramide very long chain fatty acid hydroxylase SCS7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,29311
Polymers35,0391
Non-polymers2,25410
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)36,86011
Polymers35,0391
Non-polymers1,82210
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)202.762, 202.762, 202.762
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: 35038.770 Da / Num. of mol.: 2 / Fragment: UNP Residues 96-384
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
#3: Sugar
ChemComp-BOG / octyl beta-D-glucopyranoside / Beta-Octylglucoside / octyl beta-D-glucoside / octyl D-glucoside / octyl glucoside


Type: D-saccharide / Mass: 292.369 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Formula: C14H28O6 / Comment: detergent*YM
IdentifierTypeProgram
b-octylglucosideIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#4: Chemical
ChemComp-TRD / TRIDECANE / LIPID FRAGMENT


Mass: 184.361 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C13H28

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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: 4.96 Å3/Da / Density % sol: 75.2 %
Crystal growTemperature: 287 K / Method: batch mode / pH: 5.6
Details: 10% PEG2000, 0.1M sodium citrate, pH 5.6, 50mM (NH4)2HPO4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1.25 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Jul 28, 2013
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.25 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. all: 42589 / Num. obs: 42246 / % possible obs: 99.2 % / Redundancy: 5.4 % / Rmerge(I) obs: 0.071 / Net I/σ(I): 12.1
Reflection shellResolution: 2.6→2.65 Å / Redundancy: 3.4 % / Rmerge(I) obs: 1.646 / Mean I/σ(I) obs: 0.8 / % possible all: 87.9

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Processing

Software
NameVersionClassification
PHENIX1.8.3_1479refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.6008→47.791 Å / SU ML: 0.4 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.38 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.239 2133 5.06 %Random selection
Rwork0.1973 ---
obs0.1993 42170 99.03 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.6008→47.791 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4591 0 268 0 4859
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0075033
X-RAY DIFFRACTIONf_angle_d1.1026785
X-RAY DIFFRACTIONf_dihedral_angle_d14.8741989
X-RAY DIFFRACTIONf_chiral_restr0.043663
X-RAY DIFFRACTIONf_plane_restr0.007803
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6008-2.66130.34931290.32982375X-RAY DIFFRACTION88
2.6613-2.72780.33921550.30332610X-RAY DIFFRACTION98
2.7278-2.80160.34681420.28332636X-RAY DIFFRACTION100
2.8016-2.8840.30241650.24732666X-RAY DIFFRACTION100
2.884-2.97710.2891520.23012668X-RAY DIFFRACTION100
2.9771-3.08350.26891390.21722685X-RAY DIFFRACTION100
3.0835-3.20690.26561430.21992676X-RAY DIFFRACTION100
3.2069-3.35280.26311280.19722669X-RAY DIFFRACTION100
3.3528-3.52950.22481400.19592702X-RAY DIFFRACTION100
3.5295-3.75060.23871480.18012681X-RAY DIFFRACTION100
3.7506-4.040.24761410.18232691X-RAY DIFFRACTION100
4.04-4.44630.19831450.18592701X-RAY DIFFRACTION100
4.4463-5.08910.22881430.17042718X-RAY DIFFRACTION100
5.0891-6.40930.23951400.19542728X-RAY DIFFRACTION100
6.4093-47.79950.21421230.19972831X-RAY DIFFRACTION100
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)
12.58260.0434-0.02630.85990.17210.108-0.12520.0673-0.66980.07060.04250.10730.1007-0.15370.00120.46460.01650.12990.72110.03760.667976.226742.7794126.9834
21.64650.39650.15960.9999-0.00161.05320.07050.24090.50130.13680.11810.1056-0.54510.1221-0.00080.53850.06870.09120.66510.09180.502763.060875.8285125.0379
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 117 through 390 )
2X-RAY DIFFRACTION2chain 'B' and (resid 117 through 391 )

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