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- PDB-5u81: Acid ceramidase (ASAH1, aCDase) from naked mole rat, Cys143Ala, u... -

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Basic information

Entry
Database: PDB / ID: 5u81
TitleAcid ceramidase (ASAH1, aCDase) from naked mole rat, Cys143Ala, uncleaved
ComponentsAcid ceramidase isoform b
KeywordsHYDROLASE / ceramidase / ceramide / ntn-hydrolase
Function / homology
Function and homology information


regulation of programmed necrotic cell death / ceramidase / N-acylsphingosine amidohydrolase activity / : / ceramide catabolic process / fatty acid amide hydrolase activity / regulation of steroid biosynthetic process / sphingosine biosynthetic process / ceramide biosynthetic process / keratinocyte differentiation ...regulation of programmed necrotic cell death / ceramidase / N-acylsphingosine amidohydrolase activity / : / ceramide catabolic process / fatty acid amide hydrolase activity / regulation of steroid biosynthetic process / sphingosine biosynthetic process / ceramide biosynthetic process / keratinocyte differentiation / fatty acid metabolic process / cellular response to tumor necrosis factor / lysosome / extracellular space / nucleus
Similarity search - Function
Acid ceramidase-like / Acid ceramidase, N-terminal / beta subunit of N-acylethanolamine-hydrolyzing acid amidase / Choloylglycine hydrolase/NAAA C-terminal / Linear amide C-N hydrolases, choloylglycine hydrolase family
Similarity search - Domain/homology
Acid ceramidase / Acid ceramidase
Similarity search - Component
Biological speciesHeterocephalus glaber (naked mole-rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.4 Å
AuthorsGebai, A. / Gorelik, A. / Illes, K. / Nagar, B.
CitationJournal: Nat Commun / Year: 2018
Title: Structural basis for the activation of acid ceramidase.
Authors: Gebai, A. / Gorelik, A. / Li, Z. / Illes, K. / Nagar, B.
History
DepositionDec 13, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 28, 2018Provider: repository / Type: Initial release
Revision 1.1May 2, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _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
Revision 1.2Apr 17, 2019Group: Data collection / Structure summary / Category: entity / Item: _entity.pdbx_ec
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_special_symmetry / pdbx_validate_close_contact / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.id / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_special_symmetry.label_asym_id / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_2 / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr2_auth_asym_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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Acid ceramidase isoform b
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,23710
Polymers44,1581
Non-polymers3,0809
Water5,459303
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Acid ceramidase isoform b
hetero molecules

A: Acid ceramidase isoform b
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,47520
Polymers88,3152
Non-polymers6,16018
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area11950 Å2
ΔGint25 kcal/mol
Surface area29540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)160.767, 53.913, 48.802
Angle α, β, γ (deg.)90.00, 104.41, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-599-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Acid ceramidase isoform b


Mass: 44157.516 Da / Num. of mol.: 1 / Fragment: UNP residues 22-395
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Heterocephalus glaber (naked mole-rat) / Gene: ASAH1 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: A0A0P6JG37, UniProt: G5AP74*PLUS, ceramidase

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Sugars , 3 types, 3 molecules

#2: Polysaccharide alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1056.964 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3[DManpa1-6]DManpb1-4DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/4,6,5/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5][a1221m-1a_1-5]/1-1-2-3-3-4/a4-b1_a6-f1_b4-c1_c3-d1_c6-e1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}}[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#3: Polysaccharide alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 910.823 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3DManpa1-6DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,5,4/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3/a4-b1_b4-c1_c6-d1_d3-e1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(6+1)][a-D-Manp]{[(3+1)][a-D-Manp]{}}}}}}LINUCSPDB-CARE
#4: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE

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Non-polymers , 5 types, 309 molecules

#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#7: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#8: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 303 / 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: 2.32 Å3/Da / Density % sol: 46.97 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / Details: MES glycerol PEG 1000 PEG 600 / PH range: 6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.9801 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Sep 17, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9801 Å / Relative weight: 1
ReflectionResolution: 1.4→37.391 Å / Num. obs: 69316 / % possible obs: 99 % / Redundancy: 3.7 % / Net I/σ(I): 27.8

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
HKL-2000data reduction
HKL-2000data scaling
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 1.4→37.391 Å / SU ML: 0.11 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 15.58
RfactorNum. reflection% reflection
Rfree0.1584 3490 5.03 %
Rwork0.1222 --
obs0.124 69316 86.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.4→37.391 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2977 0 203 303 3483
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083361
X-RAY DIFFRACTIONf_angle_d1.1744597
X-RAY DIFFRACTIONf_dihedral_angle_d15.921319
X-RAY DIFFRACTIONf_chiral_restr0.078540
X-RAY DIFFRACTIONf_plane_restr0.007553
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4-1.41920.2578700.16631339X-RAY DIFFRACTION45
1.4192-1.43950.2525850.15821595X-RAY DIFFRACTION53
1.4395-1.4610.2082970.14641816X-RAY DIFFRACTION60
1.461-1.48380.19861080.14581911X-RAY DIFFRACTION63
1.4838-1.50810.18471020.1372050X-RAY DIFFRACTION68
1.5081-1.53410.18141260.13742165X-RAY DIFFRACTION72
1.5341-1.5620.20331230.132273X-RAY DIFFRACTION76
1.562-1.59210.17951320.12392450X-RAY DIFFRACTION81
1.5921-1.62460.17991410.12252569X-RAY DIFFRACTION85
1.6246-1.65990.19141360.12082671X-RAY DIFFRACTION89
1.6599-1.69850.1631490.11352731X-RAY DIFFRACTION91
1.6985-1.7410.1661440.11342848X-RAY DIFFRACTION93
1.741-1.78810.14631570.10922902X-RAY DIFFRACTION97
1.7881-1.84070.15571600.10723034X-RAY DIFFRACTION100
1.8407-1.90010.14941580.10763003X-RAY DIFFRACTION100
1.9001-1.9680.13731600.10223042X-RAY DIFFRACTION100
1.968-2.04680.16271590.10173000X-RAY DIFFRACTION100
2.0468-2.13990.14921600.09683069X-RAY DIFFRACTION100
2.1399-2.25270.14251590.09683009X-RAY DIFFRACTION100
2.2527-2.39380.15061590.09593022X-RAY DIFFRACTION100
2.3938-2.57860.14021620.10753065X-RAY DIFFRACTION100
2.5786-2.83810.15021590.1183041X-RAY DIFFRACTION100
2.8381-3.24850.15421610.12983066X-RAY DIFFRACTION100
3.2485-4.0920.14791610.12933058X-RAY DIFFRACTION100
4.092-37.40470.17321620.16073097X-RAY DIFFRACTION99

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