[English] 日本語
Yorodumi
- PDB-1g85: CRYSTAL STRUCTURE OF BOVINE ODORANT BINDING PROTEIN COMPLEXED WIT... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1g85
TitleCRYSTAL STRUCTURE OF BOVINE ODORANT BINDING PROTEIN COMPLEXED WITH IS NATURAL LIGAND
ComponentsODORANT-BINDING PROTEIN
KeywordsSIGNALING PROTEIN / lipocalin / swapping domain / homodimer
Function / homology
Function and homology information


odorant binding / small molecule binding / sensory perception of smell / extracellular space
Similarity search - Function
Lipocalin, OBP-like / Lipocalin / Lipocalin family conserved site / Lipocalin / cytosolic fatty-acid binding protein family / Lipocalin/cytosolic fatty-acid binding domain / Calycin beta-barrel core domain / Calycin / Lipocalin / Lipocalin signature. / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
(3R)-oct-1-en-3-ol / Odorant-binding protein
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsVincent, F. / Spinelli, S. / Cambillau, C. / Tegoni, M.
Citation
Journal: J.Biol.Chem. / Year: 2001
Title: The insect attractant 1-octen-3-ol is the natural ligand of bovine odorant-binding protein.
Authors: Ramoni, R. / Vincent, F. / Grolli, S. / Conti, V. / Malosse, C. / Boyer, F.D. / Nagnan-Le Meillour, P. / Spinelli, S. / Cambillau, C. / Tegoni, M.
#1: Journal: Nat.Struct.Biol. / Year: 1996
Title: Domain swapping creates a third putative combining site in bovine odorant binding protein dimer.
Authors: Tegoni, M. / Spinelli, S. / Cambillau, C. / Spinelli, S.
History
DepositionNov 16, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 26, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 5, 2014Group: Non-polymer description
Revision 1.4Aug 9, 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 / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: ODORANT-BINDING PROTEIN
B: ODORANT-BINDING PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,4256
Polymers36,9132
Non-polymers5134
Water2,702150
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6470 Å2
ΔGint-4 kcal/mol
Surface area16330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.9, 65.5, 42.7
Angle α, β, γ (deg.)90, 98.8, 90
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein ODORANT-BINDING PROTEIN


Mass: 18456.318 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / References: UniProt: P07435
#2: Chemical
ChemComp-3OL / (3R)-oct-1-en-3-ol


Mass: 128.212 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H16O
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 150 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.09 Å3/Da / Density % sol: 41.21 %
Crystal growTemperature: 277 K / Method: microdialysis / pH: 5.7
Details: 38% ethanol, 25mM sodium citrate, pH 5.7, MICRODIALYSIS, temperature 4K, temperature 277K

-
Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: May 23, 2000 / Details: osmic mirrors
RadiationMonochromator: osmic mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→55 Å / Num. all: 237362 / Num. obs: 107952 / % possible obs: 45 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 4 % / Biso Wilson estimate: 35.94 Å2 / Rmerge(I) obs: 0.084 / Net I/σ(I): 5
Reflection shellResolution: 1.8→55 Å / Redundancy: 4 % / Rmerge(I) obs: 0.23 / Num. unique all: 27620 / % possible all: 97.8

-
Processing

Software
NameVersionClassification
CNSrefinement
DENZOdata reduction
CCP4(SCALA)data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1PBO

1pbo


Resolution: 1.8→25.3 Å / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.228 1309 RANDOM
Rwork0.203 --
all0.264 27646 -
obs0.203 26967 -
Displacement parametersBiso mean: 42.8 Å2
Baniso -1Baniso -2Baniso -3
1--0.84 Å20 Å2-0.11 Å2
2---5.3 Å20 Å2
3---6.14 Å2
Refine analyzeLuzzati coordinate error obs: 0.21 Å / Luzzati d res low obs: 5 Å / Luzzati sigma a obs: 0.12 Å
Refinement stepCycle: LAST / Resolution: 1.8→25.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2581 0 36 150 2767
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_d1.4
X-RAY DIFFRACTIONc_dihedral_angle_d26.8
X-RAY DIFFRACTIONc_improper_angle_d2.12
LS refinement shellResolution: 1.8→1.91 Å / Rfactor Rfree error: 0.02
RfactorNum. reflection% reflection
Rfree0.297 215 -
Rwork0.264 --
obs-4315 98 %

+
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