[English] 日本語
Yorodumi
- PDB-3d75: Crystal structure of a pheromone binding protein mutant D35N, fro... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3d75
TitleCrystal structure of a pheromone binding protein mutant D35N, from Apis mellifera, at pH 5.5
ComponentsPheromone-binding protein ASP1
KeywordsPheromone Binding Protein / Honey bee / Apis mellifera / signal transduction / queen mandibular protein / pH
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
N-BUTYL-BENZENESULFONAMIDE / Pheromone-binding protein ASP1
Similarity search - Component
Biological speciesApis mellifera (honey bee)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 2.3 Å
AuthorsPesenti, M.E. / Spinelli, S. / Bezirard, V. / Briand, L. / Pernollet, J.C. / Tegoni, M. / Cambillau, C.
Citation
Journal: J.Mol.Biol. / Year: 2009
Title: Queen bee pheromone binding protein pH-induced domain swapping favors pheromone release
Authors: Pesenti, M.E. / Spinelli, S. / Bezirard, V. / Briand, L. / Pernollet, J.C. / Campanacci, V. / Tegoni, M. / Cambillau, C.
#1: Journal: To be Published
Title: The pH Driven Domain-swapping Dimerization of Queen Bee ASP1 Favours Pheromone Release
Authors: Pesenti, M.E. / Spinelli, S. / Bezirard, V. / Briand, L. / Pernollet, J.C. / Tegoni, M. / Cambillau, C.
History
DepositionMay 20, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 26, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 10, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 1, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.4Oct 30, 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)13,4072
Polymers13,1941
Non-polymers2131
Water1,00956
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)78.547, 83.737, 47.875
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-124-

HOH

21A-135-

HOH

31A-145-

HOH

41A-160-

HOH

-
Components

#1: Protein Pheromone-binding protein ASP1


Mass: 13193.804 Da / Num. of mol.: 1 / Fragment: UNP residues 26-144 / Mutation: D35N
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-NBB / N-BUTYL-BENZENESULFONAMIDE


Mass: 213.297 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15NO2S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 56 / 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: 2.98 Å3/Da / Density % sol: 58.77 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 1.3M ammonium sulfate, 67mM sodium citrate, 33mM SPG buffer, 8.3% PEG1500, pH5.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.542 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jan 15, 2008 / Details: polar mirror
RadiationMonochromator: Osmic vacuum / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.542 Å / Relative weight: 1
ReflectionResolution: 2.3→30.36 Å / Num. all: 7140 / Num. obs: 7140 / % possible obs: 98.4 % / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Biso Wilson estimate: 45.63 Å2 / Rmerge(I) obs: 0.056 / Rsym value: 0.056 / Net I/σ(I): 16.5
Reflection shellResolution: 2.3→2.42 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.39 / Mean I/σ(I) obs: 3.1 / Num. unique all: 1040 / Rsym value: 0.39 / % possible all: 99.8

-
Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MAR345dtbdata collection
MOSFLMdata reduction
SCALAdata scaling
REFMAC5.2.0019phasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB ENTRY 2H8V

2h8v


Resolution: 2.3→30 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.926 / SU B: 11.808 / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.264 / ESU R Free: 0.201 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21548 696 9.8 %RANDOM
Rwork0.17746 ---
all0.18098 6435 --
obs0.18098 6435 97.64 %-
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: 57.219 Å2
Baniso -1Baniso -2Baniso -3
1--0.3 Å20 Å20 Å2
2--1.61 Å20 Å2
3----1.32 Å2
Refine analyzeLuzzati sigma a free: 0.201 Å
Refinement stepCycle: LAST / Resolution: 2.3→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms907 0 14 56 977
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.022940
X-RAY DIFFRACTIONr_bond_other_d0.0010.02609
X-RAY DIFFRACTIONr_angle_refined_deg1.941.9821281
X-RAY DIFFRACTIONr_angle_other_deg1.4363.0081498
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4745116
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.20627.11145
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.96515156
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.932152
X-RAY DIFFRACTIONr_chiral_restr0.230.2144
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021046
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02162
X-RAY DIFFRACTIONr_nbd_refined0.2170.2242
X-RAY DIFFRACTIONr_nbd_other0.190.2613
X-RAY DIFFRACTIONr_nbtor_refined0.1820.2470
X-RAY DIFFRACTIONr_nbtor_other0.0940.2477
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2050.245
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.220.218
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2520.232
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2320.26
X-RAY DIFFRACTIONr_mcbond_it0.6181.5758
X-RAY DIFFRACTIONr_mcbond_other0.1391.5233
X-RAY DIFFRACTIONr_mcangle_it0.7932950
X-RAY DIFFRACTIONr_scbond_it1.3263409
X-RAY DIFFRACTIONr_scangle_it1.8134.5331
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.242 52 -
Rwork0.22 466 -
obs-466 99.62 %

+
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