[English] 日本語
Yorodumi
- PDB-3bfb: Crystal structure of a pheromone binding protein from Apis mellif... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3bfb
TitleCrystal structure of a pheromone binding protein from Apis mellifera in complex with the 9-keto-2(E)-decenoic acid
ComponentsPheromone-binding protein ASP1
KeywordsPHEROMONE BINDING PROTEIN / Honeybee / Apis mellifera / signal transduction / queen mandibular pheromone / PHEROMONE-BINDING PROTEIN
Function / homology
Function and homology information


odorant binding / sensory perception of smell / extracellular space
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
(2Z)-9-oxodec-2-enoic acid / Pheromone-binding protein ASP1
Similarity search - Component
Biological speciesApis mellifera (honey bee)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.15 Å
AuthorsPesenti, M.E. / Spinelli, S. / Bezirard, V. / Briand, L. / Pernollet, J.C. / Tegoni, M. / Cambillau, C.
CitationJournal: J.Mol.Biol. / Year: 2008
Title: Structural basis of the honey bee PBP pheromone and pH-induced conformational change
Authors: Pesenti, M.E. / Spinelli, S. / Bezirard, V. / Briand, L. / Pernollet, J.C. / Tegoni, M. / Cambillau, C.
History
DepositionNov 21, 2007Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 10, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_special_symmetry / 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
Revision 1.3Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Pheromone-binding protein ASP1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,5995
Polymers13,1951
Non-polymers4044
Water1,08160
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Pheromone-binding protein ASP1
hetero molecules

A: Pheromone-binding protein ASP1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,19710
Polymers26,3902
Non-polymers8088
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area1680 Å2
ΔGint-32 kcal/mol
Surface area12570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.099, 84.281, 47.602
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-120-

CL

21A-136-

HOH

31A-180-

HOH

41A-181-

HOH

-
Components

#1: Protein Pheromone-binding protein ASP1


Mass: 13194.789 Da / Num. of mol.: 1 / Fragment: UNP residues 26-144
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Apis mellifera (honey bee) / Plasmid: pHIL-D2 / Production host: Pichia pastoris (fungus) / References: UniProt: Q9U9J6
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-9OD / (2Z)-9-oxodec-2-enoic acid / 9-keto-2(E)-decenoic acid


Mass: 184.232 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16O3
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 60 / 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: 2.97 Å3/Da / Density % sol: 58.56 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 1.7M ammonium sulfate, 0.1M sodium citrate, pH5.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 8, 2007 / Details: cylindrical grazing incidence mirror
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.15→57.3 Å / Num. obs: 9124 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 6.9 % / Biso Wilson estimate: 43.67 Å2 / Rmerge(I) obs: 0.072 / Rsym value: 0.072 / Net I/σ(I): 16.6
Reflection shellResolution: 2.15→2.27 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.492 / Mean I/σ(I) obs: 3.8 / Num. unique all: 1273 / Rsym value: 0.492 / % possible all: 100

-
Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
ADSCQuantumdata collection
MOSFLMdata reduction
SCALAdata scaling
REFMAC5.2.0019phasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB ENTRY 1R5R

1r5r
PDB Unreleased entry


Resolution: 2.15→40 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.932 / SU B: 13.783 / SU ML: 0.183 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.229 / ESU R Free: 0.199 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25223 882 10 %RANDOM
Rwork0.20353 ---
all0.20848 7975 --
obs0.20848 7975 99.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 40.979 Å2
Baniso -1Baniso -2Baniso -3
1-1.69 Å20 Å20 Å2
2---0.13 Å20 Å2
3----1.56 Å2
Refine analyzeLuzzati coordinate error free: 0.199 Å
Refinement stepCycle: LAST / Resolution: 2.15→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms907 0 26 60 993
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.022958
X-RAY DIFFRACTIONr_bond_other_d0.0030.02630
X-RAY DIFFRACTIONr_angle_refined_deg1.2791.9861300
X-RAY DIFFRACTIONr_angle_other_deg0.9623.0081553
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3845116
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.56527.17446
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.91715161
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.712152
X-RAY DIFFRACTIONr_chiral_restr0.0740.2146
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021055
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02160
X-RAY DIFFRACTIONr_nbd_refined0.2260.2237
X-RAY DIFFRACTIONr_nbd_other0.1940.2646
X-RAY DIFFRACTIONr_nbtor_refined0.1770.2484
X-RAY DIFFRACTIONr_nbtor_other0.0890.2460
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.20.246
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1530.211
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2280.230
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.380.213
X-RAY DIFFRACTIONr_mcbond_it0.6411.5763
X-RAY DIFFRACTIONr_mcbond_other0.1281.5234
X-RAY DIFFRACTIONr_mcangle_it0.722959
X-RAY DIFFRACTIONr_scbond_it1.1873418
X-RAY DIFFRACTIONr_scangle_it1.5834.5341
LS refinement shellResolution: 2.15→2.206 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.347 73 -
Rwork0.263 571 -
obs-571 100 %
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)
17.0753-0.05995.86612.2023-0.54767.24760.09730.33831.2662-0.0199-0.6046-0.50120.21860.80970.5073-0.19130.00930.1631-0.23640.0806-0.067911.496411.7757-4.2664
211.96330.85040.1711.15363.673912.2682-0.1112-1.34811.2122-0.1088-1.1163-0.5931-0.94751.0411.22750.1786-0.1526-0.1570.2107-0.2650.350419.98517.14479.7404
38.51440.35886.45298.0555-0.73815.2153-0.4926-1.48172.05240.3054-0.5459-0.4187-0.9019-0.51681.0386-0.2228-0.0552-0.0161-0.0228-0.29860.11647.251315.91365.292
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA3 - 693 - 69
2X-RAY DIFFRACTION2AA70 - 8870 - 88
3X-RAY DIFFRACTION3AA89 - 11989 - 119

+
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