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- PDB-5w7c: Human acyloxyacyl hydrolase (AOAH), proteolytically processed, S2... -

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Basic information

Entry
Database: PDB / ID: 5w7c
TitleHuman acyloxyacyl hydrolase (AOAH), proteolytically processed, S263A mutant, with LPS
Components(Acyloxyacyl hydrolase) x 2
KeywordsHYDROLASE / lipopolysaccharide / LPS / GDSL esterase / saposin
Function / homology
Function and homology information


lipopolysaccharide catabolic process / acyloxyacyl hydrolase / acyloxyacyl hydrolase activity / fatty acid metabolic process / negative regulation of inflammatory response / cytoplasmic vesicle / calcium ion binding / extracellular region
Similarity search - Function
Acyloxyacyl hydrolase / : / Saposin-like domain / Saposin-like type B, region 2 / Saposin (B) Domains / GDSL lipase/esterase / Saposin B type domain / Saposin-like / Saposin B type domain profile. / GDSL-like Lipase/Acylhydrolase / SGNH hydrolase superfamily
Similarity search - Domain/homology
LAURIC ACID / 3-HYDROXY-TETRADECANOIC ACID / Acyloxyacyl hydrolase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.23 Å
AuthorsGorelik, A. / Illes, K. / 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: Crystal structure of the mammalian lipopolysaccharide detoxifier.
Authors: Gorelik, A. / Illes, K. / Nagar, B.
History
DepositionJun 19, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 3, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2018Group: Database references / Category: citation
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
Revision 1.2Jan 31, 2018Group: Database references / Category: citation
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.3Feb 14, 2018Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.4Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / 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_conn_angle / 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 / _chem_comp.name / _chem_comp.type / _pdbx_entity_nonpoly.entity_id / _pdbx_entity_nonpoly.name / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _struct_conn.conn_type_id / _struct_conn.id / _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.ptnr1_label_seq_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
Revision 2.1Oct 30, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Acyloxyacyl hydrolase
C: Acyloxyacyl hydrolase
B: Acyloxyacyl hydrolase
D: Acyloxyacyl hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)132,69326
Polymers128,0044
Non-polymers4,69022
Water5,314295
1
A: Acyloxyacyl hydrolase
C: Acyloxyacyl hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,34713
Polymers64,0022
Non-polymers2,34511
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6000 Å2
ΔGint-5 kcal/mol
Surface area24230 Å2
MethodPISA
2
B: Acyloxyacyl hydrolase
D: Acyloxyacyl hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,34713
Polymers64,0022
Non-polymers2,34511
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6010 Å2
ΔGint-7 kcal/mol
Surface area24770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.170, 104.080, 145.280
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 2 types, 4 molecules ABCD

#1: Protein Acyloxyacyl hydrolase


Mass: 15831.375 Da / Num. of mol.: 2 / Fragment: N-terminal residues 24-152
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: AOAH / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P28039, acyloxyacyl hydrolase
#2: Protein Acyloxyacyl hydrolase


Mass: 48170.438 Da / Num. of mol.: 2 / Fragment: C-terminal residues 153-575 / Mutation: S263A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: AOAH / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P28039, acyloxyacyl hydrolase

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Sugars , 2 types, 8 molecules

#3: 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.: 4
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
#4: 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.: 4
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, 309 molecules

#5: Chemical
ChemComp-FTT / 3-HYDROXY-TETRADECANOIC ACID / 3-HYDROXY-MYRISTIC ACID


Mass: 244.370 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Formula: C14H28O3
#6: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Ca
#7: Chemical ChemComp-DAO / LAURIC ACID


Mass: 200.318 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H24O2
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 295 / Source method: isolated from a natural source / Formula: H2O

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Details

Compound detailsThe authors state that the protein was proteolytically cleaved likely between residues 152-153.
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: 2.6 Å3/Da / Density % sol: 52.78 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: post-chymotrypsin; 1mM Triton X-100, 0.333 mM E. coli LPS Ra; 200 mM ammonium chloride, 100 mM sodium acetate pH 5.3, 20 % PEG 6000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97243 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: May 23, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97243 Å / Relative weight: 1
ReflectionResolution: 2.23→50 Å / Num. obs: 61346 / % possible obs: 100 % / Redundancy: 13.6 % / Net I/σ(I): 9.4

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.23→44.816 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.92 / Phase error: 27.08 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2451 6296 5.01 %
Rwork0.2115 --
obs0.2132 125758 99.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.23→44.816 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8478 0 302 295 9075
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0029020
X-RAY DIFFRACTIONf_angle_d0.62112233
X-RAY DIFFRACTIONf_dihedral_angle_d12.685387
X-RAY DIFFRACTIONf_chiral_restr0.0411342
X-RAY DIFFRACTIONf_plane_restr0.0031547
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.23-2.25530.33092110.34483983X-RAY DIFFRACTION100
2.2553-2.28190.33952070.34093966X-RAY DIFFRACTION100
2.2819-2.30970.35522140.33434051X-RAY DIFFRACTION100
2.3097-2.33890.35692070.32863935X-RAY DIFFRACTION100
2.3389-2.36970.36962080.31534005X-RAY DIFFRACTION100
2.3697-2.40220.31522080.30323987X-RAY DIFFRACTION100
2.4022-2.43650.33312120.29614021X-RAY DIFFRACTION100
2.4365-2.47290.34382070.28143939X-RAY DIFFRACTION100
2.4729-2.51150.3072120.26384009X-RAY DIFFRACTION100
2.5115-2.55270.27362060.2553967X-RAY DIFFRACTION100
2.5527-2.59670.27032160.24064022X-RAY DIFFRACTION100
2.5967-2.64390.27762050.23763904X-RAY DIFFRACTION100
2.6439-2.69470.26392110.24254027X-RAY DIFFRACTION100
2.6947-2.74970.2892110.23753981X-RAY DIFFRACTION100
2.7497-2.80950.28432100.23953984X-RAY DIFFRACTION100
2.8095-2.87490.24972080.22423973X-RAY DIFFRACTION100
2.8749-2.94670.26922140.2283969X-RAY DIFFRACTION100
2.9467-3.02640.25722140.22644030X-RAY DIFFRACTION100
3.0264-3.11540.2632090.21583930X-RAY DIFFRACTION100
3.1154-3.2160.23332100.22154005X-RAY DIFFRACTION100
3.216-3.33090.24242100.21473979X-RAY DIFFRACTION100
3.3309-3.46420.27122140.20444001X-RAY DIFFRACTION100
3.4642-3.62180.20012040.19713973X-RAY DIFFRACTION100
3.6218-3.81260.23542110.1773984X-RAY DIFFRACTION100
3.8126-4.05140.16982090.16663973X-RAY DIFFRACTION100
4.0514-4.36390.16412100.15233981X-RAY DIFFRACTION100
4.3639-4.80260.18522120.15763925X-RAY DIFFRACTION99
4.8026-5.49650.22692080.17224007X-RAY DIFFRACTION100
5.4965-6.92090.22482120.19843989X-RAY DIFFRACTION100
6.9209-44.82510.27372060.20933962X-RAY DIFFRACTION99

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