[English] 日本語
Yorodumi
- PDB-2wcm: Structure of BMori GOBP2 (General Odorant Binding Protein 2) with... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2wcm
TitleStructure of BMori GOBP2 (General Odorant Binding Protein 2) with (10E)-hexadecen-12-yn-1-ol
ComponentsGENERAL ODORANT-BINDING PROTEIN 1
KeywordsTRANSPORT PROTEIN / ODORANT BINDING PROTEIN / OLFACTION / TRANSPORT / DISULFIDE BOND / INSECT PHEREMONE / SENSORY TRANSDUCTION
Function / homology
Function and homology information


odorant binding / sensory perception of smell
Similarity search - Function
Odorant/pheromone binding protein, Lepidoptera / 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
(10E)-hexadec-10-en-12-yn-1-ol / General odorant-binding protein 2
Similarity search - Component
Biological speciesBOMBYX MORI (domestic silkworm)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsRobertson, G. / Zhou, J.-J. / He, X. / Pickett, J.A. / Field, L.M. / Keep, N.H.
CitationJournal: J.Mol.Biol. / Year: 2009
Title: Characterisation of Bombyx Mori Odorant-Binding Proteins Reveals that a General Odorant-Binding Protein Discriminates between Sex Pheromone Components.
Authors: Zhou, J.-J. / Robertson, G. / He, X. / Dufour, S. / Hooper, A.M. / Pickett, J.A. / Keep, N.H. / Field, L.M.
History
DepositionMar 12, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 11, 2009Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id / _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: GENERAL ODORANT-BINDING PROTEIN 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,4724
Polymers16,1871
Non-polymers2853
Water2,072115
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)33.209, 33.209, 189.363
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

-
Components

#1: Protein GENERAL ODORANT-BINDING PROTEIN 1 / GENERAL ODORANT BINDING PROTEIN 2 / GOBP2 / GOBP1


Mass: 16187.409 Da / Num. of mol.: 1 / Fragment: RESIDUES 20-160
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) BOMBYX MORI (domestic silkworm) / Organ: ANTENNA / Plasmid: PET17B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P34170
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-B9M / (10E)-hexadec-10-en-12-yn-1-ol


Mass: 236.393 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H28O
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 115 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHREE POINT MUTATIONS DUE TO STRAIN DIFFERENCES. THE CDNA USED FOR THIS EXPERIMENT WAS OBTAINED ...THREE POINT MUTATIONS DUE TO STRAIN DIFFERENCES. THE CDNA USED FOR THIS EXPERIMENT WAS OBTAINED FROM THE STRAIN DAZAO. THE DIFFERENCES ARE NATURALLY OCCURING BETWEEN THE STRAIN USED FOR THIS WORK AND THAT USED FOR P34170 WHICH HAS THE SAME SEQUENCE FOR GOBP2 AS THE GENOME SEQUENCED STRAIN P50

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 1.87 Å3/Da / Density % sol: 34 % / Description: NONE
Crystal growpH: 8.5 / Details: 30% PEG 4000, 200MM MGCL2, 100MM TRIS PH 8.5

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97
DetectorType: ADSC CCD / Detector: CCD / Date: Jun 30, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 1.5→63.2 Å / Num. obs: 17328 / % possible obs: 92.9 % / Observed criterion σ(I): 0 / Redundancy: 6.4 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 14.8
Reflection shellResolution: 1.5→1.54 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.38 / Mean I/σ(I) obs: 3.8 / % possible all: 95.4

-
Processing

Software
NameVersionClassification
REFMAC5.5.0088refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2WC5

2wc5


Resolution: 1.5→62.5 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.93 / SU B: 1.734 / SU ML: 0.066 / Cross valid method: THROUGHOUT / ESU R: 0.097 / ESU R Free: 0.1 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.U VALUES
RfactorNum. reflection% reflectionSelection details
Rfree0.24 928 4.9 %RANDOM
Rwork0.197 ---
obs0.199 18084 92.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.34 Å2
Baniso -1Baniso -2Baniso -3
1-0.27 Å20.14 Å20 Å2
2--0.27 Å20 Å2
3----0.41 Å2
Refinement stepCycle: LAST / Resolution: 1.5→62.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1126 0 19 115 1260
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0221197
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.981.951611
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1855150
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.47524.91559
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.33915227
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.321156
X-RAY DIFFRACTIONr_chiral_restr0.1370.2176
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.02890
X-RAY DIFFRACTIONr_gen_planes_other
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_it1.3711.5718
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.14321168
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.4823479
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it5.7594.5438
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.5→1.54 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.307 79 -
Rwork0.247 1287 -
obs--95.73 %

+
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