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- PDB-6yxh: Cryogenic human alkaline ceramidase 3 (ACER3) at 2.6 A resolution... -

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Basic information

Entry
Database: PDB / ID: 6yxh
TitleCryogenic human alkaline ceramidase 3 (ACER3) at 2.6 A resolution determined by Serial Crystallography (SSX) using CrystalDirect
ComponentsAlkaline ceramidase 3
KeywordsMEMBRANE PROTEIN / Alkaline ceramidase / ACER3 / serial synchrotron crystallography / SSX / CrystalDirect / LCP crystallisation / in meso / HTX facility / Membrane proteins
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 / inflammatory response / Golgi membrane / calcium ion binding / positive regulation of cell population proliferation / endoplasmic reticulum membrane / zinc ion binding / membrane
Similarity search - Function
Alkaline ceramidase / Ceramidase
Similarity search - Domain/homology
Alkaline ceramidase 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsHealey, R.D. / Basu, S. / Humm, A.S. / Leyrat, C. / Dupeux, F. / Pica, A. / Granier, S. / Marquez, J.A.
Funding supportEuropean Union, 3items
OrganizationGrant numberCountry
European Research Council (ERC)647687European Union
European Commission653706European Union
European Commission871037European Union
CitationJournal: Cell Rep Methods / Year: 2021
Title: An automated platform for structural analysis of membrane proteins through serial crystallography.
Authors: Healey, R.D. / Basu, S. / Humm, A.S. / Leyrat, C. / Cong, X. / Golebiowski, J. / Dupeux, F. / Pica, A. / Granier, S. / Marquez, J.A.
History
DepositionMay 1, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 12, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 17, 2021Group: Advisory / Data collection / Database references
Category: citation / citation_author ...citation / citation_author / database_2 / pdbx_database_proc / pdbx_unobs_or_zero_occ_atoms
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Jan 24, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Alkaline ceramidase 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,26813
Polymers40,4911
Non-polymers77612
Water1,08160
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1290 Å2
ΔGint-119 kcal/mol
Surface area19850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.47, 69.97, 259.49
Angle α, β, γ (deg.)90, 90, 90
Int Tables number20
Space group name H-MC2221

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Alkaline ceramidase 3 / Alkaline CDase 3 / Alkaline dihydroceramidase SB89 / Alkaline phytoceramidase / aPHC


Mass: 40491.059 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ACER3, APHC, PHCA / Production host: Spodoptera frugiperda / Variant (production host): BOLD-2017
References: UniProt: Q9NUN7, Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides, ceramidase

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Non-polymers , 6 types, 72 molecules

#2: Chemical ChemComp-ZN / ZINC ION


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


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


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 60 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 3.45 Å3/Da / Density % sol: 64.3 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase
Details: 30 or 50 nl bolus overlaid with 600 nl precipitant solution in CrystalDirect plate-2. 41% PEG 400, 100 mM HEPES pH 7.5, 75 mM magnesium sulfate and 5% DMSO. Crystallisation experiments were ...Details: 30 or 50 nl bolus overlaid with 600 nl precipitant solution in CrystalDirect plate-2. 41% PEG 400, 100 mM HEPES pH 7.5, 75 mM magnesium sulfate and 5% DMSO. Crystallisation experiments were carried out at the HTX facility of EMBL Grenoble. LCP bolus were harvested automatically at cryogenic condition using CrystalDirect technology.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: Y
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.988 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 23, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.988 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 17701 / % possible obs: 100 % / Redundancy: 36.01 % / CC1/2: 0.99 / Net I/σ(I): 8.4
Reflection shellResolution: 2.6→2.62 Å / Mean I/σ(I) obs: 0.98 / Num. unique obs: 1275 / CC1/2: 0.33
Serial crystallography sample deliveryMethod: fixed target

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Processing

Software
NameVersionClassification
BUSTER2.10.3 (6-FEB-2020)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6G7O

6g7o


Resolution: 2.6→46.18 Å / Cor.coef. Fo:Fc: 0.855 / Cor.coef. Fo:Fc free: 0.839 / SU R Cruickshank DPI: 0.424 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.428 / SU Rfree Blow DPI: 0.294 / SU Rfree Cruickshank DPI: 0.296
RfactorNum. reflection% reflectionSelection details
Rfree0.28 885 -RANDOM
Rwork0.2315 ---
obs0.234 17701 100 %-
Displacement parametersBiso mean: 84.84 Å2
Baniso -1Baniso -2Baniso -3
1--21.6831 Å20 Å20 Å2
2--4.1797 Å20 Å2
3---17.5034 Å2
Refine analyzeLuzzati coordinate error obs: 0.42 Å
Refinement stepCycle: LAST / Resolution: 2.6→46.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2855 0 36 60 2951
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.012959HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.064028HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d988SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes478HARMONIC5
X-RAY DIFFRACTIONt_it2959HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion380SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact2373SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion2.93
X-RAY DIFFRACTIONt_other_torsion20.35
LS refinement shellResolution: 2.6→2.62 Å
RfactorNum. reflection% reflection
Rfree0.3495 20 -
Rwork0.3224 --
obs0.3237 403 100 %
Refinement TLS params.Origin x: 20.4852 Å / Origin y: 5.6041 Å / Origin z: -40.0276 Å
111213212223313233
T-0.1525 Å20.0515 Å2-0.0192 Å2--0.1305 Å20.0177 Å2---0.1095 Å2
L0.8482 °2-0.1087 °20.4773 °2-1.3296 °20.8393 °2--2.2172 °2
S-0.0832 Å °0.5342 Å °0.1547 Å °0.5342 Å °0.1157 Å °-0.2209 Å °0.1547 Å °-0.2209 Å °-0.0325 Å °
Refinement TLS groupSelection details: { A|* }

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