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- PDB-5w78: Human acyloxyacyl hydrolase (AOAH), proteolytically processed -

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Basic information

Entry
Database: PDB / ID: 5w78
TitleHuman acyloxyacyl hydrolase (AOAH), proteolytically processed
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 / intracellular membrane-bounded organelle / calcium ion binding / extracellular region
Similarity search - Function
Acyloxyacyl hydrolase / GDSL lipase/esterase / Saposin B type, region 2 / 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
LAURIC ACID / MYRISTIC ACID / PALMITIC ACID / Acyloxyacyl hydrolase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.271 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 / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_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

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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)66,28511
Polymers64,0182
Non-polymers2,2679
Water3,171176
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, monomer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7640 Å2
ΔGint-29 kcal/mol
Surface area24310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.402, 87.356, 146.510
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, 2 molecules AB

#1: Protein Acyloxyacyl hydrolase


Mass: 15831.375 Da / Num. of mol.: 1 / 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: 48186.438 Da / Num. of mol.: 1 / Fragment: C-terminal residues 153-575
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 , 1 types, 3 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.: 3
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

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Non-polymers , 5 types, 182 molecules

#4: Chemical ChemComp-MYR / MYRISTIC ACID


Mass: 228.371 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H28O2 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-PLM / PALMITIC ACID


Mass: 256.424 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H32O2 / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical ChemComp-DAO / LAURIC ACID


Mass: 200.318 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H24O2 / Feature type: SUBJECT OF INVESTIGATION
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 176 / Source method: isolated from a natural source / Formula: H2O

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Details

Compound detailsThe authors state that the protein is proteolytically cleaved likely between residues 152-153.

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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: 2.52 Å3/Da / Density % sol: 51.19 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: post-chymotrypsin; 100 mM sodium citrate pH 5, 20 % PEG 6000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 1.90745 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Dec 8, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.90745 Å / Relative weight: 1
ReflectionResolution: 2.27→50 Å / Num. obs: 30265 / % possible obs: 99 % / Redundancy: 10.8 % / Net I/σ(I): 15.6

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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: 2.271→47.661 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.78
RfactorNum. reflection% reflection
Rfree0.2007 2074 5.04 %
Rwork0.1659 --
obs0.1676 41152 71.28 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.271→47.661 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4193 0 150 176 4519
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0064461
X-RAY DIFFRACTIONf_angle_d0.7526045
X-RAY DIFFRACTIONf_dihedral_angle_d12.2162676
X-RAY DIFFRACTIONf_chiral_restr0.044662
X-RAY DIFFRACTIONf_plane_restr0.004762
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2706-2.32340.3208510.2935975X-RAY DIFFRACTION27
2.3234-2.38150.2922690.26911302X-RAY DIFFRACTION35
2.3815-2.44590.2906770.24241472X-RAY DIFFRACTION40
2.4459-2.51790.29880.21441672X-RAY DIFFRACTION45
2.5179-2.59910.2339940.20461792X-RAY DIFFRACTION50
2.5991-2.6920.21361030.1971980X-RAY DIFFRACTION54
2.692-2.79980.22791180.19822308X-RAY DIFFRACTION62
2.7998-2.92720.21181430.19032669X-RAY DIFFRACTION73
2.9272-3.08150.21031710.18273169X-RAY DIFFRACTION87
3.0815-3.27450.22381870.16533493X-RAY DIFFRACTION96
3.2745-3.52730.20631970.16763619X-RAY DIFFRACTION99
3.5273-3.88210.18451960.14813697X-RAY DIFFRACTION100
3.8821-4.44350.18591940.1293620X-RAY DIFFRACTION100
4.4435-5.5970.15921960.14313666X-RAY DIFFRACTION100
5.597-47.67110.19891900.17553644X-RAY DIFFRACTION100

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