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- PDB-5w7d: Murine acyloxyacyl hydrolase (AOAH), S262A mutant -

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Basic information

Entry
Database: PDB / ID: 5w7d
TitleMurine acyloxyacyl hydrolase (AOAH), S262A mutant
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
: / Saposin-like domain / Acyloxyacyl hydrolase / 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
MYRISTIC ACID / 1,2-DISTEAROYL-SN-GLYCERO-3-PHOSPHATE / Acyloxyacyl hydrolase
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 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_validate_close_contact / 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.pdbx_formal_charge / _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_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_seq_id_1 / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Acyloxyacyl hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,24910
Polymers64,0341
Non-polymers2,2159
Water11,566642
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, monomer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)46.527, 98.590, 73.488
Angle α, β, γ (deg.)90.00, 99.68, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Acyloxyacyl hydrolase


Mass: 64034.176 Da / Num. of mol.: 1 / 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

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Sugars , 2 types, 3 molecules

#2: 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.: 2
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


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, 648 molecules

#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-PX8 / 1,2-DISTEAROYL-SN-GLYCERO-3-PHOSPHATE


Mass: 703.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C39H76O8P
#7: Chemical ChemComp-MYR / MYRISTIC ACID


Mass: 228.371 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H28O2
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 642 / 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: 2.59 Å3/Da / Density % sol: 52.6 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 100 mM sodium acetate pH 4.6, 15% PEG 20000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97949 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Aug 1, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 1.75→50 Å / Num. obs: 66110 / % possible obs: 100 % / Redundancy: 7.4 % / Net I/σ(I): 24.4

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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: 1.75→38.703 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 17.87 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1815 2924 5 %
Rwork0.1524 --
obs0.1539 58482 88.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.75→38.703 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4218 0 143 642 5003
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0114588
X-RAY DIFFRACTIONf_angle_d1.0326251
X-RAY DIFFRACTIONf_dihedral_angle_d12.42797
X-RAY DIFFRACTIONf_chiral_restr0.057679
X-RAY DIFFRACTIONf_plane_restr0.007804
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.75-1.77870.3076640.24571239X-RAY DIFFRACTION41
1.7787-1.80940.2585810.23321521X-RAY DIFFRACTION51
1.8094-1.84230.2199910.22391738X-RAY DIFFRACTION59
1.8423-1.87770.25131050.2131991X-RAY DIFFRACTION67
1.8777-1.91610.24121150.20052204X-RAY DIFFRACTION75
1.9161-1.95770.23011310.19452470X-RAY DIFFRACTION83
1.9577-2.00330.21951440.17882731X-RAY DIFFRACTION92
2.0033-2.05340.20121530.18062913X-RAY DIFFRACTION98
2.0534-2.10890.1951560.17252955X-RAY DIFFRACTION100
2.1089-2.17090.20451540.16352949X-RAY DIFFRACTION100
2.1709-2.2410.19031580.15372995X-RAY DIFFRACTION100
2.241-2.32110.19821590.14082987X-RAY DIFFRACTION100
2.3211-2.4140.19061550.14222948X-RAY DIFFRACTION100
2.414-2.52380.17981540.13642986X-RAY DIFFRACTION100
2.5238-2.65690.16711590.13852967X-RAY DIFFRACTION100
2.6569-2.82330.17491550.1362976X-RAY DIFFRACTION100
2.8233-3.04120.16511570.14032976X-RAY DIFFRACTION100
3.0412-3.34710.16051580.14032989X-RAY DIFFRACTION100
3.3471-3.83110.1741580.1342998X-RAY DIFFRACTION100
3.8311-4.82530.12771570.12722976X-RAY DIFFRACTION100
4.8253-38.71280.18971600.16833049X-RAY DIFFRACTION100
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)
10.08190.0370.02520.21950.01060.27340.0548-0.0059-0.0680.1511-0.0328-0.19220.18830.1256-0.03840.16-0.011-0.02370.10260.00630.1109-6.078-35.1569126.067
20.0228-0.0935-0.00940.4873-0.11760.22210.11160.13440.00530.0379-0.0732-0.2286-0.01410.21710.05120.115-0.0015-0.02190.25340.04670.21013.9691-26.0165125.8106
30.44010.0216-0.07431.0423-0.28151.1340.0010.0559-0.0167-0.1363-0.0663-0.02860.07370.0346-0.0717-0.02890.01730.02490.0196-0.00260.0373-17.5101-16.6494100.6549
40.12480.0314-0.09390.63620.19340.3015-0.14110.00660.0414-0.37720.01260.3811-0.248-0.3257-0.285-0.14030.06250.06540.151-0.00450.0756-27.6249-9.6563101.4359
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 35 through 99 )
2X-RAY DIFFRACTION2chain 'A' and (resid 100 through 176 )
3X-RAY DIFFRACTION3chain 'A' and (resid 177 through 487 )
4X-RAY DIFFRACTION4chain 'A' and (resid 488 through 574 )

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