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- PDB-5w7a: Rabbit acyloxyacyl hydrolase (AOAH), proteolytically processed, S... -

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Basic information

Entry
Database: PDB / ID: 5w7a
TitleRabbit acyloxyacyl hydrolase (AOAH), proteolytically processed, S262A mutant, with LPS (low quality saposin domain)
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 / GDSL lipase/esterase / Saposin-like type B, region 2 / GDSL-like Lipase/Acylhydrolase / Saposin (B) Domains / Saposin B type domain / Saposin-like / Saposin B type domain profile. / SGNH hydrolase superfamily
Similarity search - Domain/homology
3-HYDROXY-TETRADECANOIC ACID / PHOSPHATE ION / Acyloxyacyl hydrolase
Similarity search - Component
Biological speciesOryctolagus cuniculus (rabbit)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.3 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: Advisory / Atomic model ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms / struct_asym / struct_conn / struct_conn_type / 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 / _pdbx_unobs_or_zero_occ_atoms.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 / _struct_conn_type.id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 6, 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 small subunit
B: Acyloxyacyl hydrolase large subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,39410
Polymers64,0072
Non-polymers1,3888
Water2,000111
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, monomer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3720 Å2
ΔGint-25 kcal/mol
Surface area22780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.578, 123.199, 125.918
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

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Acyloxyacyl hydrolase ... , 2 types, 2 molecules AB

#1: Protein Acyloxyacyl hydrolase small subunit


Mass: 16384.969 Da / Num. of mol.: 1 / Fragment: residues 23-153
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryctolagus cuniculus (rabbit) / Gene: AOAH / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: O18823, acyloxyacyl hydrolase
#2: Protein Acyloxyacyl hydrolase large subunit


Mass: 47621.781 Da / Num. of mol.: 1 / Fragment: residues 154-575 / Mutation: S262A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryctolagus cuniculus (rabbit) / Gene: AOAH / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: O18823, acyloxyacyl hydrolase

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Sugars , 2 types, 2 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.: 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
#5: 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.: 1
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 , 5 types, 117 molecules

#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4 / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical ChemComp-P6G / HEXAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400


Mass: 282.331 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H26O7 / Comment: precipitant*YM
#8: Chemical ChemComp-FTT / 3-HYDROXY-TETRADECANOIC ACID / 3-HYDROXY-MYRISTIC ACID


Mass: 244.370 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H28O3 / Feature type: SUBJECT OF INVESTIGATION
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 111 / Source method: isolated from a natural source / Formula: H2O

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Details

Compound detailsThe author states that the protein was treated with trypsin, and the exact cut site is unknown but ...The author states that the protein was treated with trypsin, and the exact cut site is unknown but should be somewhere between K129 and R153.
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: 2.71 Å3/Da / Density % sol: 54.69 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: post-trypsin; 1 mM Triton X-100, 0.333 mM E. coli LPS Ra; 1 M sodium citrate pH 7

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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: 2.3→50 Å / Num. obs: 31484 / % possible obs: 100 % / Redundancy: 15 % / Net I/σ(I): 45

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155)refinement
HKL-2000data reduction
HKL-2000data scaling
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 2.3→34.686 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.77
RfactorNum. reflection% reflection
Rfree0.2615 1530 5 %
Rwork0.2401 --
obs0.2412 30589 97.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.3→34.686 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3821 0 85 111 4017
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0044005
X-RAY DIFFRACTIONf_angle_d0.7465439
X-RAY DIFFRACTIONf_dihedral_angle_d13.0552386
X-RAY DIFFRACTIONf_chiral_restr0.044598
X-RAY DIFFRACTIONf_plane_restr0.004694
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3002-2.37440.34161100.31072093X-RAY DIFFRACTION78
2.3744-2.45920.30551390.29572627X-RAY DIFFRACTION98
2.4592-2.55770.27791390.28062648X-RAY DIFFRACTION100
2.5577-2.6740.29311410.28062680X-RAY DIFFRACTION100
2.674-2.81490.30811410.26812674X-RAY DIFFRACTION100
2.8149-2.99120.28551410.27212684X-RAY DIFFRACTION100
2.9912-3.2220.25071420.25072686X-RAY DIFFRACTION100
3.222-3.5460.24861410.23562687X-RAY DIFFRACTION100
3.546-4.05840.26821440.21372727X-RAY DIFFRACTION100
4.0584-5.11050.20861440.20062738X-RAY DIFFRACTION100
5.1105-34.690.24621480.21462815X-RAY DIFFRACTION99
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)
10.2498-0.50590.29271.7982-0.23050.4814-0.53591.16340.3615-1.18630.4113-0.2617-0.01240.29450.58751.1216-0.7144-0.09861.27920.38830.406127.001644.968426.3343
24.11931.2787-0.59442.8814-0.10931.2985-0.4488-0.22320.6642-0.30180.2184-0.018-0.23960.17010.25490.2245-0.0333-0.16830.0262-0.02240.294538.596848.998360.2929
34.16581.57780.43372.37020.35332.5709-0.4999-0.18030.3109-0.31320.1859-0.011-0.1528-0.31050.18560.15950.1084-0.07960.0919-0.02120.183128.920939.931460.2763
43.8041.93510.41871.25090.5282.1896-0.5441-0.26310.6363-0.15690.16760.3364-0.309-0.59850.25120.19930.0366-0.11350.269-0.0390.280718.470339.951958.2974
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 37:127 ) OR ( CHAIN B AND RESID 169:177 )A37 - 127
2X-RAY DIFFRACTION1( CHAIN A AND RESID 37:127 ) OR ( CHAIN B AND RESID 169:177 )B169 - 177
3X-RAY DIFFRACTION2( CHAIN B AND RESID 178:305 )B178 - 305
4X-RAY DIFFRACTION3( CHAIN B AND RESID 306:388 )B306 - 388
5X-RAY DIFFRACTION4( CHAIN B AND RESID 389:575 )B389 - 575

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