[English] 日本語
Yorodumi
- PDB-1oof: Complex of Drosophila odorant binding protein LUSH with ethanol -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1oof
TitleComplex of Drosophila odorant binding protein LUSH with ethanol
Componentsodorant binding protein LUSH
KeywordsTRANSPORT PROTEIN / LUSH / Alcohol / Odorant Binding
Function / homology
Function and homology information


diphenyl phthalate binding / dibutyl phthalate binding / response to pheromone / courtship behavior / pheromone binding / olfactory behavior / odorant binding / sensory perception of smell / response to ethanol / extracellular region
Similarity search - Function
Pheromone/general odorant binding protein domain / Insect pheromone/odorant binding protein domains. / Pheromone/general odorant binding protein / PBP/GOBP family / Pheromone/general odorant binding protein superfamily / Recoverin; domain 1 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
ACETATE ION / ETHANOL / General odorant-binding protein lush
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.49 Å
AuthorsKruse, S.W. / Zhao, R. / Smith, D.P. / Jones, D.N.M.
CitationJournal: Nat.Struct.Biol. / Year: 2003
Title: Structure of a specific alcohol-binding site defined by the odorant binding protein LUSH from Drosophila melanogaster
Authors: Kruse, S.W. / Zhao, R. / Smith, D.P. / Jones, D.N.M.
History
DepositionMar 3, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 2, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: odorant binding protein LUSH
B: odorant binding protein LUSH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,7598
Polymers28,4312
Non-polymers3286
Water4,216234
1
A: odorant binding protein LUSH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,3804
Polymers14,2161
Non-polymers1643
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: odorant binding protein LUSH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,3804
Polymers14,2161
Non-polymers1643
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)46.942, 46.942, 111.540
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43

-
Components

#1: Protein odorant binding protein LUSH


Mass: 14215.508 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Strain: Oregon R / Tissue: subset of trichoid olfactory sensilla / Gene: lush / Plasmid: pET28a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: O02372
#2: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-EOH / ETHANOL


Mass: 46.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 234 / 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: 2.16 Å3/Da / Density % sol: 43.06 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: PEG 4000, sodium acetate, ethanol, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal grow
*PLUS
Temperature: 4 or 18 ℃ / pH: 4 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
1100 mMsodium acetate1reservoirpH4.0
225-30 %(w/v)PEG40001reservoir
30.3 %(v/v)alcohol1reservoir

-
Data collection

DiffractionMean temperature: 105 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97895 Å
DetectorType: SBC-1 / Detector: CCD / Date: Feb 21, 2002 / Details: Mirrors
RadiationMonochromator: SI 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97895 Å / Relative weight: 1
ReflectionResolution: 1.49→30 Å / Num. all: 39458 / Num. obs: 38748 / % possible obs: 98.2 % / Observed criterion σ(I): -3 / Redundancy: 3.1 % / Rmerge(I) obs: 0.039 / Net I/σ(I): 25.4
Reflection shellResolution: 1.49→1.54 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.196 / Mean I/σ(I) obs: 2.5 / Num. unique all: 3918 / % possible all: 99.5
Reflection
*PLUS
Num. measured all: 119487
Reflection shell
*PLUS
% possible obs: 99.5 %

-
Processing

Software
NameVersionClassification
REFMAC5refinement
HKL-2000data reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 1.49→30 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.947 / SU B: 2.155 / SU ML: 0.081 / Isotropic thermal model: isotropic temperature factors / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.085 / ESU R Free: 0.085 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21002 3785 10 %RANDOM
Rwork0.17821 ---
all0.18135 35363 --
obs0.18135 33970 96.06 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 17.19 Å2
Baniso -1Baniso -2Baniso -3
1-0.03 Å20 Å20 Å2
2--0.03 Å20 Å2
3----0.06 Å2
Refinement stepCycle: LAST / Resolution: 1.49→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2030 0 16 240 2286
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0222094
X-RAY DIFFRACTIONr_bond_other_d0.0020.021892
X-RAY DIFFRACTIONr_angle_refined_deg1.4451.9762804
X-RAY DIFFRACTIONr_angle_other_deg1.03634460
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.4813246
X-RAY DIFFRACTIONr_dihedral_angle_2_deg14.82315441
X-RAY DIFFRACTIONr_chiral_restr0.0830.2298
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022244
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02400
X-RAY DIFFRACTIONr_nbd_refined0.2320.3481
X-RAY DIFFRACTIONr_nbd_other0.1920.31741
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1390.5151
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0180.51
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2150.310
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2370.345
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1560.525
X-RAY DIFFRACTIONr_mcbond_it1.031.51272
X-RAY DIFFRACTIONr_mcangle_it1.83222056
X-RAY DIFFRACTIONr_scbond_it3.0153822
X-RAY DIFFRACTIONr_scangle_it4.9784.5748
LS refinement shellResolution: 1.49→1.57 Å / Total num. of bins used: 10
RfactorNum. reflection
Rfree0.239 569
Rwork0.201 4766
obs-5330
Software
*PLUS
Version: 5 / Classification: refinement
Refinement
*PLUS
% reflection Rfree: 10 % / Rfactor Rfree: 0.21 / Rfactor Rwork: 0.178
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.015
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.445

+
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