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- PDB-5w7e: Murine acyloxyacyl hydrolase (AOAH), S262A mutant, with dimyristo... -

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Basic information

Entry
Database: PDB / ID: 5w7e
TitleMurine acyloxyacyl hydrolase (AOAH), S262A mutant, with dimyristoyl phosphatidylcholine
ComponentsAcyloxyacyl hydrolase
KeywordsHYDROLASE / lipopolysaccharide / LPS / GDSL esterase / saposin
Function / homology
Function and homology information


lipopolysaccharide catabolic process / acyloxyacyl hydrolase / acyloxyacyl hydrolase activity / lipopolysaccharide metabolic process / 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
(2S)-3-hydroxypropane-1,2-diyl ditetradecanoate / Acyloxyacyl hydrolase
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.83 Å
AuthorsGorelik, A. / Illes, K. / Nagar, B.
Funding support Canada, 1items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR)MOP-113535 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 1.5Jul 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_conn_type / 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.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 / _struct_conn_type.id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.6Nov 20, 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 / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)130,21914
Polymers128,0682
Non-polymers2,15112
Water16,736929
1
A: Acyloxyacyl hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,1107
Polymers64,0341
Non-polymers1,0756
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Acyloxyacyl hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,1107
Polymers64,0341
Non-polymers1,0756
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)81.425, 85.373, 93.398
Angle α, β, γ (deg.)90.00, 103.64, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Acyloxyacyl hydrolase


Mass: 64034.176 Da / Num. of mol.: 2 / Fragment: residues 23-574 / Mutation: S262A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Aoah / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: O35298, acyloxyacyl hydrolase
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#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.: 4
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6 / Feature type: SUBJECT OF INVESTIGATION
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
#4: Chemical ChemComp-FAW / (2S)-3-hydroxypropane-1,2-diyl ditetradecanoate


Mass: 512.805 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C31H60O5 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 929 / Source method: isolated from a natural source / Formula: H2O
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: 2.46 Å3/Da / Density % sol: 50.07 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 1 mM Triton X-100, 2 mM dimyristoyl phosphatidylcholine; 100 mM sodium MES pH 6, 15% PEG 20000

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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: 1.83→50 Å / Num. obs: 106148 / % possible obs: 100 % / Redundancy: 3.8 % / Net I/σ(I): 19.9

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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 / Resolution: 1.83→40.073 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 20.33
RfactorNum. reflection% reflection
Rfree0.1978 2616 2.06 %
Rwork0.157 --
obs0.1578 126969 58.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.83→40.073 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8370 0 134 929 9433
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0088946
X-RAY DIFFRACTIONf_angle_d0.89312193
X-RAY DIFFRACTIONf_dihedral_angle_d13.9595458
X-RAY DIFFRACTIONf_chiral_restr0.0521323
X-RAY DIFFRACTIONf_plane_restr0.0061577
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.83-1.86330.2411330.23891570X-RAY DIFFRACTION14
1.8633-1.89910.2517450.23262108X-RAY DIFFRACTION19
1.8991-1.93790.2667600.23132892X-RAY DIFFRACTION26
1.9379-1.980.2474750.22493557X-RAY DIFFRACTION32
1.98-2.02610.2271910.21684331X-RAY DIFFRACTION39
2.0261-2.07680.27061060.20545086X-RAY DIFFRACTION46
2.0768-2.13290.26681160.25527X-RAY DIFFRACTION50
2.1329-2.19570.20721180.18595625X-RAY DIFFRACTION51
2.1957-2.26650.20291190.17855672X-RAY DIFFRACTION51
2.2665-2.34750.1971180.1735707X-RAY DIFFRACTION52
2.3475-2.44150.16831310.16186224X-RAY DIFFRACTION56
2.4415-2.55260.18641540.15287051X-RAY DIFFRACTION64
2.5526-2.68720.20751680.15428154X-RAY DIFFRACTION73
2.6872-2.85550.20321970.15459263X-RAY DIFFRACTION83
2.8555-3.07590.17612150.154310154X-RAY DIFFRACTION92
3.0759-3.38530.20082160.146910316X-RAY DIFFRACTION93
3.3853-3.87480.16612110.138210222X-RAY DIFFRACTION92
3.8748-4.88050.18612150.126710202X-RAY DIFFRACTION92
4.8805-40.08230.21262280.162110692X-RAY DIFFRACTION96
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.14420.05550.00160.09210.01960.0801-0.03560.26940.1517-0.16140.04730.1084-0.0479-0.06350.01350.18370.0238-0.0670.20330.01140.1709-7.5035.9763-54.8256
2-0.0022-0.0018-0.00110.0477-0.0130.0233-0.12790.13930.1382-0.00840.0349-0.1229-0.06390.013200.3831-0.0197-0.04040.37190.06140.347-12.40115.6381-47.4477
30.3165-0.30640.30210.83510.08460.714-0.1588-0.2465-0.23320.21650.00050.7438-0.0243-0.48-0.5548-0.11680.09180.09130.1430.01410.1915-22.5287-4.1383-20.6588
40.03010.07120.08620.20620.23620.2853-0.0793-0.0495-0.13020.0405-0.04470.17990.0174-0.1087-0.17080.06060.0210.03030.09320.02590.1375-12.9939-8.1171-20.6435
50.5293-0.0635-0.16920.4007-0.09480.3452-0.0406-0.1575-0.19220.1512-0.1157-0.0896-0.09070.068-0.56690.12310.0133-0.02390.06230.02410.0078-1.05342.3919-20.8268
60.089-0.1172-0.04560.1790.04390.20050.0083-0.14590.03970.1890.0335-0.17620.07350.21240.0990.1281-0.0445-0.12840.19130.04770.0656-45.559.0196-40.8035
70.09330.05210.03450.3401-0.13650.1012-0.052-0.03190.0620.1759-0.0509-0.0767-0.15520.0917-0.26550.1244-0.0717-0.06180.16110.03240.2036-43.604715.2436-53.5727
80.61980.54970.18851.0188-0.3860.8515-0.19840.2141-0.4547-0.255-0.0096-0.76990.25070.4682-0.8848-0.20140.11830.12240.03250.11720.2156-32.5966-9.6891-70.0031
90.63270.1439-0.26060.4446-0.00320.609-0.13830.154-0.2802-0.22-0.1136-0.00580.0358-0.0368-1.21620.1154-0.0270.02290.03210.02340.023-49.4709-1.6753-74.7528
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 35 through 128 )
2X-RAY DIFFRACTION2chain 'A' and (resid 129 through 177 )
3X-RAY DIFFRACTION3chain 'A' and (resid 178 through 292 )
4X-RAY DIFFRACTION4chain 'A' and (resid 293 through 337 )
5X-RAY DIFFRACTION5chain 'A' and (resid 338 through 574 )
6X-RAY DIFFRACTION6chain 'B' and (resid 35 through 99 )
7X-RAY DIFFRACTION7chain 'B' and (resid 100 through 197 )
8X-RAY DIFFRACTION8chain 'B' and (resid 198 through 325 )
9X-RAY DIFFRACTION9chain 'B' and (resid 326 through 574 )

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