[English] 日本語
Yorodumi
- PDB-6p2e: Structure of Aedes aegypti OBP22 in the complex with benzaldehyde -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6p2e
TitleStructure of Aedes aegypti OBP22 in the complex with benzaldehyde
ComponentsOBP22, AAEL005772-PA
KeywordsTRANSPORT PROTEIN / Odorant binding protein / Chemo-sensory signaling
Function / homology
Function and homology information


odorant binding / sensory perception of smell / lipid binding / :
Similarity search - Function
Insect pheromone/odorant binding protein domains. / Pheromone/general odorant binding protein / PBP/GOBP family / Pheromone/general odorant binding protein superfamily
Similarity search - Domain/homology
BENZOIC ACID / Odorant-binding protein 22
Similarity search - Component
Biological speciesAedes aegypti (yellow fever mosquito)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsJones, D.N. / Murphy, E.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI121253 United States
CitationJournal: Sci Rep / Year: 2020
Title: Aedes aegypti Odorant Binding Protein 22 selectively binds fatty acids through a conformational change in its C-terminal tail.
Authors: Wang, J. / Murphy, E.J. / Nix, J.C. / Jones, D.N.M.
History
DepositionMay 21, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 31, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2May 6, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.3Apr 3, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: OBP22, AAEL005772-PA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,8996
Polymers14,4001
Non-polymers4985
Water1,982110
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: assay for oligomerization, NMR relaxation experiments establish the overall correlation time is consistent with the presence of a monomeric species in solution. The dimeric form appears to ...Evidence: assay for oligomerization, NMR relaxation experiments establish the overall correlation time is consistent with the presence of a monomeric species in solution. The dimeric form appears to be a crystallization artifact.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)86.934, 86.934, 58.515
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-205-

SO4

21A-308-

HOH

31A-341-

HOH

-
Components

#1: Protein OBP22, AAEL005772-PA / Odorant binding protein


Mass: 14400.319 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aedes aegypti (yellow fever mosquito) / Tissue: Antennal cDNA / Gene: 5567053, AAEL005772 / Plasmid: pET13a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q1HRL7
#2: Chemical ChemComp-BEZ / BENZOIC ACID


Mass: 122.121 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H6O2
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 110 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 4.61 Å3/Da / Density % sol: 73.4 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 2M Ammonium sulfate, 0.1 M sodium citrate, 0.2M sodium potassium tartrate

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1 Å
DetectorType: RDI CMOS_8M / Detector: CMOS / Date: Sep 13, 2013 / Details: Rosenbaum-Rock monochromator
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→35 Å / Num. obs: 40781 / % possible obs: 99.69 % / Redundancy: 2 % / Biso Wilson estimate: 30.72 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.01588 / Rpim(I) all: 0.01588 / Rrim(I) all: 0.02246 / Net I/σ(I): 25.63
Reflection shellResolution: 1.9→1.968 Å / Redundancy: 2 % / Rmerge(I) obs: 0.2494 / Mean I/σ(I) obs: 3.16 / Num. unique obs: 2001 / CC1/2: 0.889 / Rpim(I) all: 0.2494 / Rrim(I) all: 0.3528 / % possible all: 99.85

-
Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
XDSdata reduction
SCALAdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: OBP22 structure solved by tantalum SAD

Resolution: 1.9→35 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.952 / SU B: 2.269 / SU ML: 0.066 / Cross valid method: THROUGHOUT / ESU R: 0.105 / ESU R Free: 0.099 / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.20013 1997 9.8 %RANDOM
Rwork0.18294 ---
obs0.18464 18421 99.57 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 35.491 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3----0.01 Å2
Refinement stepCycle: 1 / Resolution: 1.9→35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms990 0 31 110 1131
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0121086
X-RAY DIFFRACTIONr_bond_other_d0.0010.0181015
X-RAY DIFFRACTIONr_angle_refined_deg1.1321.6381472
X-RAY DIFFRACTIONr_angle_other_deg0.3951.5912314
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3275131
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.98723.38762
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.66115190
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.353156
X-RAY DIFFRACTIONr_chiral_restr0.0590.2137
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021242
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02268
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.263.21509
X-RAY DIFFRACTIONr_mcbond_other2.2633.2508
X-RAY DIFFRACTIONr_mcangle_it3.394.785642
X-RAY DIFFRACTIONr_mcangle_other3.3874.798643
X-RAY DIFFRACTIONr_scbond_it3.153.632577
X-RAY DIFFRACTIONr_scbond_other3.1233.584570
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.9735.22818
X-RAY DIFFRACTIONr_long_range_B_refined6.58538.4751292
X-RAY DIFFRACTIONr_long_range_B_other6.58238.4841293
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.898→1.947 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.253 141 -
Rwork0.255 1322 -
obs--97.99 %

+
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