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- PDB-6g7o: Crystal structure of human alkaline ceramidase 3 (ACER3) at 2.7 A... -

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Basic information

Entry
Database: PDB / ID: 6g7o
TitleCrystal structure of human alkaline ceramidase 3 (ACER3) at 2.7 Angstrom resolution
ComponentsAlkaline ceramidase 3,Soluble cytochrome b562
KeywordsMEMBRANE PROTEIN / Hydrolase / 7TM / Zinc binding protein / Calcium-binding protein
Function / homology
Function and homology information


: / phytosphingosine biosynthetic process / : / ceramidase / N-acylsphingosine amidohydrolase activity / : / ceramide catabolic process / regulation of programmed cell death / sphingosine biosynthetic process / sphingolipid biosynthetic process ...: / phytosphingosine biosynthetic process / : / ceramidase / N-acylsphingosine amidohydrolase activity / : / ceramide catabolic process / regulation of programmed cell death / sphingosine biosynthetic process / sphingolipid biosynthetic process / Sphingolipid de novo biosynthesis / Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides / myelination / electron transport chain / periplasmic space / electron transfer activity / inflammatory response / iron ion binding / Golgi membrane / calcium ion binding / heme binding / positive regulation of cell population proliferation / endoplasmic reticulum membrane / zinc ion binding / membrane
Similarity search - Function
Alkaline ceramidase / Ceramidase / Cytochrome b562 / Cytochrome b562 / Cytochrome c/b562
Similarity search - Domain/homology
(2S)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / Soluble cytochrome b562 / Alkaline ceramidase 3
Similarity search - Component
Biological speciesHomo sapiens (human)
Escherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.7 Å
AuthorsLeyrat, C. / Vasiliauskaite-Brooks, I. / Healey, R.D. / Sounier, R. / Grison, C. / Hoh, F. / Basu, S. / Granier, S.
Funding support France, 1items
OrganizationGrant numberCountry
European Commission647687 France
CitationJournal: Nat Commun / Year: 2018
Title: Structure of a human intramembrane ceramidase explains enzymatic dysfunction found in leukodystrophy.
Authors: Vasiliauskaite-Brooks, I. / Healey, R.D. / Rochaix, P. / Saint-Paul, J. / Sounier, R. / Grison, C. / Waltrich-Augusto, T. / Fortier, M. / Hoh, F. / Saied, E.M. / Arenz, C. / Basu, S. / Leyrat, C. / Granier, S.
History
DepositionApr 6, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 2, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Alkaline ceramidase 3,Soluble cytochrome b562
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,64715
Polymers40,4911
Non-polymers1,15614
Water2,198122
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1450 Å2
ΔGint-135 kcal/mol
Surface area19530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.880, 68.830, 257.520
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-413-

MG

21A-593-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Alkaline ceramidase 3,Soluble cytochrome b562 / Alkaline CDase 3 / Alkaline dihydroceramidase SB89 / Alkaline phytoceramidase / aPHC / Cytochrome b-562


Mass: 40491.059 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human), (gene. exp.) Escherichia coli (E. coli)
Gene: ACER3, APHC, PHCA, cybC / Production host: Spodoptera frugiperda (fall armyworm) / Variant (production host): Sf9
References: UniProt: Q9NUN7, UniProt: P0ABE7, Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides

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Non-polymers , 7 types, 136 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-OLB / (2S)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate


Mass: 356.540 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H40O4
#6: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#7: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 122 / 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: 3.33 Å3/Da / Density % sol: 63.08 % / Description: ~ 20 x 20 x 30 micrometers , rectangular
Crystal growTemperature: 293.15 K / Method: lipidic cubic phase / pH: 7.5 / Details: 75mM MgSO4, 34-40% PEG400, 5% DMSO

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.00001 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 8, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00001 Å / Relative weight: 1
ReflectionResolution: 2.7→45.6 Å / Num. obs: 15327 / % possible obs: 100 % / Redundancy: 27.6 % / Biso Wilson estimate: 64.64 Å2 / CC1/2: 0.964 / Rmerge(I) obs: 0.566 / Rpim(I) all: 0.11 / Rrim(I) all: 0.577 / Net I/σ(I): 8.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
2.7-2.8327.74.49119800.4960.8654.575100
8.96-45.6260.1244740.960.0290.12899.3

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
BUSTER2.10.3refinement
XDSdata reduction
Aimless0.5.32data scaling
PHASERphasing
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4RWD plus fragments derived from an I-TASSER ab-initio model

4rwd


Resolution: 2.7→45.6 Å / Cor.coef. Fo:Fc: 0.861 / Cor.coef. Fo:Fc free: 0.873 / SU R Cruickshank DPI: 0.652 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.723 / SU Rfree Blow DPI: 0.325 / SU Rfree Cruickshank DPI: 0.323
RfactorNum. reflection% reflectionSelection details
Rfree0.27 716 4.67 %RANDOM
Rwork0.248 ---
obs0.249 15325 100 %-
Displacement parametersBiso max: 217.86 Å2 / Biso mean: 74.44 Å2 / Biso min: 31.53 Å2
Baniso -1Baniso -2Baniso -3
1--14.1731 Å20 Å20 Å2
2--1.798 Å20 Å2
3---12.3752 Å2
Refine analyzeLuzzati coordinate error obs: 0.46 Å
Refinement stepCycle: final / Resolution: 2.7→45.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2855 0 62 122 3039
Biso mean--99.73 57.08 -
Num. residues----350
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1009SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes480HARMONIC5
X-RAY DIFFRACTIONt_it2984HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion381SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact3679SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d2984HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg4055HARMONIC20.97
X-RAY DIFFRACTIONt_omega_torsion2.06
X-RAY DIFFRACTIONt_other_torsion19.3
LS refinement shellResolution: 2.7→2.73 Å / Rfactor Rfree error: 0 / Total num. of bins used: 35
RfactorNum. reflection% reflection
Rfree0.2054 24 5.48 %
Rwork0.2483 414 -
all0.2459 438 -
obs--99.54 %
Refinement TLS params.Method: refined / Origin x: -10.244 Å / Origin y: 5.6067 Å / Origin z: -39.5298 Å
111213212223313233
T-0.1496 Å20.0871 Å2-0.0178 Å2--0.1509 Å20.04 Å2---0.211 Å2
L0.859 °2-0.0779 °20.5247 °2-1.0726 °20.6963 °2--2.7114 °2
S-0.0956 Å °-0.4465 Å °-0.0783 Å °0.4546 Å °0.094 Å °0.0138 Å °0.0561 Å °-0.3971 Å °0.0016 Å °
Refinement TLS groupSelection details: { A|* }

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