[English] 日本語
Yorodumi
- PDB-5w7b: Rabbit acyloxyacyl hydrolase (AOAH), proteolytically processed, S... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5w7b
TitleRabbit acyloxyacyl hydrolase (AOAH), proteolytically processed, S262A 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 / cytoplasmic vesicle / calcium ion binding / extracellular region
Similarity search - Function
Acyloxyacyl hydrolase / GDSL lipase/esterase / Saposin B type, region 2 / Saposin-like type B, region 2 / Saposin (B) Domains / GDSL-like Lipase/Acylhydrolase / Saposin B type domain / Saposin-like / Saposin B type domain profile. / SGNH hydrolase superfamily
Similarity search - Domain/homology
3-HYDROXY-TETRADECANOIC ACID / MYRISTIC ACID / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / PHOSPHATE ION / Acyloxyacyl hydrolase
Similarity search - Component
Biological speciesOryctolagus cuniculus (rabbit)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 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 / Data collection / Category: chem_comp / pdbx_audit_support
Item: _chem_comp.type / _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_struct_special_symmetry / pdbx_validate_close_contact / 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_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_special_symmetry.label_asym_id / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Acyloxyacyl hydrolase small subunit
C: Acyloxyacyl hydrolase large subunit
B: Acyloxyacyl hydrolase small subunit
D: Acyloxyacyl hydrolase large subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)139,33964
Polymers128,0144
Non-polymers11,32660
Water8,071448
1
A: Acyloxyacyl hydrolase small subunit
C: Acyloxyacyl hydrolase large subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,07236
Polymers64,0072
Non-polymers6,06534
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14290 Å2
ΔGint50 kcal/mol
Surface area23580 Å2
MethodPISA
2
B: Acyloxyacyl hydrolase small subunit
D: Acyloxyacyl hydrolase large subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,26828
Polymers64,0072
Non-polymers5,26126
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12140 Å2
ΔGint24 kcal/mol
Surface area23800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)109.522, 138.806, 89.530
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11D-867-

HOH

-
Components

-
Acyloxyacyl hydrolase ... , 2 types, 4 molecules ABCD

#1: Protein Acyloxyacyl hydrolase small subunit /


Mass: 16384.969 Da / Num. of mol.: 2 / 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.: 2 / 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

-
Sugars , 4 types, 8 molecules

#3: Polysaccharide alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 367.349 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
LFucpa1-6DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-2/a6-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#4: Polysaccharide 3-deoxy-alpha-D-manno-oct-2-ulopyranosonic acid-(2-6)-2-amino-2-deoxy-beta-D-glucopyranose-(1-6)-2- ...3-deoxy-alpha-D-manno-oct-2-ulopyranosonic acid-(2-6)-2-amino-2-deoxy-beta-D-glucopyranose-(1-6)-2-amino-2-deoxy-alpha-D-glucopyranose


Type: oligosaccharide / Mass: 560.504 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DKdopa2-6DGlcpNb1-6DGlcpNa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,3,2/[a2122h-1a_1-5_2*N][a2122h-1b_1-5_2*N][Aad1122h-2a_2-6]/1-2-3/a6-b1_b6-c2WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpN]{[(6+1)][b-D-GlcpN]{[(6+2)][a-D-Kdop]{}}}LINUCSPDB-CARE
#5: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 570.542 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-1-2/a4-b1_a6-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#6: 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

-
Non-polymers , 10 types, 500 molecules

#7: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C4H10O3
#8: Chemical
ChemComp-PGE / TRIETHYLENE GLYCOL / Polyethylene glycol


Mass: 150.173 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C6H14O4
#9: Chemical
ChemComp-FTT / 3-HYDROXY-TETRADECANOIC ACID / 3-HYDROXY-MYRISTIC ACID


Mass: 244.370 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C14H28O3 / Feature type: SUBJECT OF INVESTIGATION
#10: Chemical
ChemComp-MYR / MYRISTIC ACID / Myristic acid


Mass: 228.371 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C14H28O2 / Feature type: SUBJECT OF INVESTIGATION
#11: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#12: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#13: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID / MES (buffer)


Mass: 195.237 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H13NO4S / Feature type: SUBJECT OF INVESTIGATION / Comment: pH buffer*YM
#14: Chemical
ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400 / Polyethylene glycol


Mass: 238.278 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H22O6 / Feature type: SUBJECT OF INVESTIGATION / Comment: precipitant*YM
#15: Chemical
ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4 / Feature type: SUBJECT OF INVESTIGATION
#16: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 448 / Source method: isolated from a natural source / Formula: H2O

-
Details

Compound detailsThe authors state that the protein was treated with trypsin, and the exact cut site is unknown but ...The authors state that the protein was treated with trypsin, and the exact cut site is unknown but should be somewhere between K129 and R153.

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.66 Å3/Da / Density % sol: 53.74 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: post-trypsin; 1 mM Triton X-100, 0.333 mM E. coli LPS Ra; 100 mM sodium MES pH 6; 34 % PEG 200; 5 % PEG 3000

-
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: 1.9→50 Å / Num. obs: 106913 / % possible obs: 100 % / Redundancy: 14.6 % / Net I/σ(I): 19.5

-
Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→44.765 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.52
RfactorNum. reflection% reflection
Rfree0.2134 2713 2.03 %
Rwork0.1849 --
obs0.1855 133760 64.37 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.9→44.765 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8055 0 728 448 9231
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0059082
X-RAY DIFFRACTIONf_angle_d0.98212245
X-RAY DIFFRACTIONf_dihedral_angle_d14.9875402
X-RAY DIFFRACTIONf_chiral_restr0.0471331
X-RAY DIFFRACTIONf_plane_restr0.0051499
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.93460.3497390.2821932X-RAY DIFFRACTION18
1.9346-1.97180.3163490.27222362X-RAY DIFFRACTION22
1.9718-2.0120.2902630.2542995X-RAY DIFFRACTION28
2.012-2.05580.2814760.24493767X-RAY DIFFRACTION35
2.0558-2.10360.3064950.2444485X-RAY DIFFRACTION42
2.1036-2.15620.28811040.23385139X-RAY DIFFRACTION48
2.1562-2.21450.24131140.22595480X-RAY DIFFRACTION51
2.2145-2.27970.21091250.21135832X-RAY DIFFRACTION54
2.2797-2.35320.23411210.20156138X-RAY DIFFRACTION57
2.3532-2.43730.21761370.19626465X-RAY DIFFRACTION61
2.4373-2.53490.22081360.19136957X-RAY DIFFRACTION65
2.5349-2.65030.20641600.18137632X-RAY DIFFRACTION71
2.6503-2.790.19681740.18248559X-RAY DIFFRACTION80
2.79-2.96480.2252030.19199855X-RAY DIFFRACTION92
2.9648-3.19360.21072240.176510674X-RAY DIFFRACTION100
3.1936-3.51490.20782230.171910687X-RAY DIFFRACTION100
3.5149-4.02320.20772210.160610725X-RAY DIFFRACTION100
4.0232-5.06770.19682220.155610706X-RAY DIFFRACTION100
5.0677-44.77740.19132270.205910657X-RAY DIFFRACTION99

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more