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- PDB-6dy2: Guinea pig N-acylethanolamine-hydrolyzing acid amidase (NAAA) cov... -

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Basic information

Entry
Database: PDB / ID: 6dy2
TitleGuinea pig N-acylethanolamine-hydrolyzing acid amidase (NAAA) covalently bound to beta-lactam inhibitor ARN726
Components(N-acylethanolamine acid amidase ...) x 2
KeywordsHYDROLASE / endocannabinoid / lipase
Function / homology
Function and homology information


: / N-(long-chain-acyl)ethanolamine deacylase / sphingosine metabolic process / N-(long-chain-acyl)ethanolamine deacylase activity / ceramidase / N-acylsphingosine amidohydrolase activity / N-acylethanolamine metabolic process / N-acylphosphatidylethanolamine metabolic process / fatty acid amide hydrolase activity / lipid catabolic process ...: / N-(long-chain-acyl)ethanolamine deacylase / sphingosine metabolic process / N-(long-chain-acyl)ethanolamine deacylase activity / ceramidase / N-acylsphingosine amidohydrolase activity / N-acylethanolamine metabolic process / N-acylphosphatidylethanolamine metabolic process / fatty acid amide hydrolase activity / lipid catabolic process / fatty acid metabolic process / lysosome / membrane
Similarity search - Function
Acid ceramidase-like / Acid ceramidase, N-terminal / beta subunit of N-acylethanolamine-hydrolyzing acid amidase / Linear amide C-N hydrolases, choloylglycine hydrolase family
Similarity search - Domain/homology
Chem-HJA / PHOSPHATE ION / N-acylethanolamine-hydrolyzing acid amidase
Similarity search - Component
Biological speciesCavia porcellus (domestic guinea pig)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.706 Å
AuthorsGorelik, A. / Gebai, A. / Illes, K. / Piomelli, D. / Nagar, B.
Funding support Canada, 1items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR)MOP-133535 Canada
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2018
Title: Molecular mechanism of activation of the immunoregulatory amidase NAAA.
Authors: Gorelik, A. / Gebai, A. / Illes, K. / Piomelli, D. / Nagar, B.
History
DepositionJul 1, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 26, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 10, 2018Group: Data collection / Database references / Structure summary
Category: citation / entity
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year / _entity.formula_weight
Revision 1.2Oct 24, 2018Group: Data collection / Database references / Structure summary
Category: citation / citation_author / entity
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed ..._citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _entity.formula_weight
Revision 1.3Nov 7, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.4Apr 17, 2019Group: Data collection / Structure summary / Category: entity / Item: _entity.pdbx_ec
Revision 1.5Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.6Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.7Oct 11, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.8Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: N-acylethanolamine acid amidase alpha-subunit
B: N-acylethanolamine acid amidase beta-subunit
C: N-acylethanolamine acid amidase alpha-subunit
D: N-acylethanolamine acid amidase beta-subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,82025
Polymers75,3084
Non-polymers2,51221
Water2,396133
1
A: N-acylethanolamine acid amidase alpha-subunit
B: N-acylethanolamine acid amidase beta-subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,92813
Polymers37,6542
Non-polymers1,27411
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5620 Å2
ΔGint-73 kcal/mol
Surface area13970 Å2
MethodPISA
2
C: N-acylethanolamine acid amidase alpha-subunit
D: N-acylethanolamine acid amidase beta-subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,89212
Polymers37,6542
Non-polymers1,23810
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5630 Å2
ΔGint-74 kcal/mol
Surface area14490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.885, 98.863, 117.761
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11C-302-

HOH

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Components

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N-acylethanolamine acid amidase ... , 2 types, 4 molecules ACBD

#1: Protein N-acylethanolamine acid amidase alpha-subunit


Mass: 11686.366 Da / Num. of mol.: 2 / Fragment: residues 21-115
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cavia porcellus (domestic guinea pig) / Gene: NAAA / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: H0VCJ6, N-(long-chain-acyl)ethanolamine deacylase
#2: Protein N-acylethanolamine acid amidase beta-subunit


Mass: 25967.422 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cavia porcellus (domestic guinea pig) / Gene: NAAA / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: H0VCJ6

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Sugars , 1 types, 6 molecules

#3: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 4 types, 148 molecules

#4: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#6: Chemical ChemComp-HJA / (2S)-3-amino-2-{[(4-cyclohexylbutoxy)carbonyl]amino}propanethioic S-acid


Mass: 302.433 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H26N2O3S / Feature type: SUBJECT OF INVESTIGATION
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 133 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 2.78 Å3/Da / Density % sol: 55.73 %
Crystal growTemperature: 293 K / Method: vapor diffusion / Details: 0.2 M KH2PO4 and 20 % PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jun 17, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.706→50 Å / Num. obs: 23122 / % possible obs: 98 % / Redundancy: 11.6 % / Net I/σ(I): 16
Reflection shellResolution: 2.706→2.8 Å

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5U7Z

5u7z


Resolution: 2.706→49.431 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.15
RfactorNum. reflection% reflection
Rfree0.2329 2848 9.7 %
Rwork0.184 --
obs0.1887 29346 66.32 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.706→49.431 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5110 0 143 133 5386
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0035386
X-RAY DIFFRACTIONf_angle_d0.6877362
X-RAY DIFFRACTIONf_dihedral_angle_d10.863150
X-RAY DIFFRACTIONf_chiral_restr0.043834
X-RAY DIFFRACTIONf_plane_restr0.003932
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7058-2.75250.3265500.3056463X-RAY DIFFRACTION23
2.7525-2.80250.3695600.2694545X-RAY DIFFRACTION28
2.8025-2.85640.2896650.2679614X-RAY DIFFRACTION31
2.8564-2.91470.2939740.2728676X-RAY DIFFRACTION34
2.9147-2.97810.2498820.2493764X-RAY DIFFRACTION38
2.9781-3.04740.3282940.2512850X-RAY DIFFRACTION43
3.0474-3.12360.27041050.2283943X-RAY DIFFRACTION47
3.1236-3.2080.22831150.21861060X-RAY DIFFRACTION53
3.208-3.30240.24421200.22151137X-RAY DIFFRACTION57
3.3024-3.40890.23961390.20781291X-RAY DIFFRACTION64
3.4089-3.53070.25571410.19511403X-RAY DIFFRACTION70
3.5307-3.67210.23751610.18031544X-RAY DIFFRACTION77
3.6721-3.83910.22191760.17171639X-RAY DIFFRACTION82
3.8391-4.04150.20761940.17151773X-RAY DIFFRACTION88
4.0415-4.29450.23982070.14831865X-RAY DIFFRACTION94
4.2945-4.62590.18832140.13191950X-RAY DIFFRACTION99
4.6259-5.0910.19992130.13792003X-RAY DIFFRACTION100
5.091-5.82670.21452170.16881997X-RAY DIFFRACTION100
5.8267-7.33710.24122150.21472006X-RAY DIFFRACTION100
7.3371-49.43970.26492060.2161975X-RAY DIFFRACTION99

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