[English] 日本語
Yorodumi
- PDB-1e02: Porcine Odorant Binding Protein Complexed with undecanal -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 100
TitlePorcine Odorant Binding Protein Complexed with undecanal
ComponentsODORANT-BINDING PROTEIN
KeywordsODORANT BINDING PROTEIN / LIPOCALINS
Function / homology
Function and homology information


odorant binding / response to stimulus / small molecule binding / sensory perception of smell / extracellular space
Similarity search - Function
Lipocalin, OBP-like / Lipocalin / Calycin beta-barrel core domain / Lipocalin / cytosolic fatty-acid binding protein family / Lipocalin/cytosolic fatty-acid binding domain / Calycin / Lipocalin / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
UNDECANAL / Odorant-binding protein
Similarity search - Component
Biological speciesSUS SCROFA (pig)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 2.15 Å
AuthorsVincent, F. / Spinelli, S. / Cambillau, C. / Tegoni, M.
CitationJournal: J.Mol.Biol. / Year: 2000
Title: Complexes of Porcine Odorant Binding Protein with Odorant Molecules Belonging to Different Chemical Classes
Authors: Vincent, F. / Spinelli, S. / Ramoni, R. / Grolli, S. / Pelosi, P. / Cambillau, C. / Tegoni, M.
History
DepositionMar 9, 2000Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 6, 2000Provider: repository / Type: Initial release
Revision 1.1May 7, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

-
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)35,7834
Polymers35,4432
Non-polymers3412
Water3,639202
1
A: ODORANT-BINDING PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,8922
Polymers17,7211
Non-polymers1701
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: ODORANT-BINDING PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,8922
Polymers17,7211
Non-polymers1701
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)41.779, 87.914, 92.507
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.16058, -0.18129, 0.97023), (-0.1754, 0.9621, 0.2088), (-0.97131, -0.20371, 0.1227)
Vector: -23.94837, 18.5359, 22.07671)

-
Components

#1: Protein ODORANT-BINDING PROTEIN / / PIG OBP


Mass: 17721.414 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) SUS SCROFA (pig) / Organ: NOSE / Tissue: OLFACTORY EPITHELIUM / References: UniProt: P81245
#2: Chemical ChemComp-UNA / UNDECANAL / Undecanal


Mass: 170.292 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H22O
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 202 / 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: 2.46 Å3/Da / Density % sol: 50 %
Crystal growpH: 7.8 / Details: 2M AMMONIUM SULFATE, AND 5% ISOPROPANOL, pH 7.80
Crystal grow
*PLUS
Temperature: 20 ℃ / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
19 mg/mlprotein1drop
22 Mammonium sulfate1reservoir
35 %(v/v)iso-propanol1reservoir

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: LURE / Beamline: DW32 / Wavelength: 0.97
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Dec 1, 1997
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 1.83→15 Å / Num. obs: 30761 / % possible obs: 97.7 % / Redundancy: 2.9 % / Biso Wilson estimate: 13.5 Å2 / Rsym value: 0.047 / Net I/σ(I): 16
Reflection shellResolution: 1.83→1.86 Å / Redundancy: 2.7 % / Mean I/σ(I) obs: 4.3 / Rsym value: 0.17 / % possible all: 96.9
Reflection
*PLUS
Highest resolution: 2.15 Å / Lowest resolution: 18 Å / % possible obs: 90.7 % / Redundancy: 3.2 % / Rmerge(I) obs: 0.079
Reflection shell
*PLUS

-
Processing

Software
NameVersionClassification
X-PLOR3.843refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3.843phasing
RefinementMethod to determine structure: OTHER / Resolution: 2.15→18 Å / Data cutoff high absF: 1000000 / Data cutoff low absF: 100 / Cross valid method: THROUGHOUT / σ(F): 0
Details: N-TERMINUS FROM RESIDUE 1 TO 8, IN SUBUNIT A AND 1 - 10 IN SUBUNIT B, ARE NOT VISIBLE IN THE ELECTRON DENSITY, DUE TO FLEXIBILITY. ALTERNATE POSITIONS ARE PRESENT FOR SIDE CHAIN OF RESIDUES ...Details: N-TERMINUS FROM RESIDUE 1 TO 8, IN SUBUNIT A AND 1 - 10 IN SUBUNIT B, ARE NOT VISIBLE IN THE ELECTRON DENSITY, DUE TO FLEXIBILITY. ALTERNATE POSITIONS ARE PRESENT FOR SIDE CHAIN OF RESIDUES 19A, 39A, 114A. THE ATOMS CONCERNED HAVE OCCUPANCY BETWEEN 0.0 AND 1.0 AND A SEGID AC1 AND AC2 OFTEN, OCCUPANCY VALUES LOWER THAN 1.0 APPEARED TO JUSTIFY BETTER THE ELECTRON DENSITY. FOR THIS REASON WE HAVE KEPT THIS LOW OCCUPANCY FOR SEVERAL SIDE CHAIN ATOMS.
RfactorNum. reflection% reflectionSelection details
Rfree0.256 870 5 %RANDOM
Rwork0.192 ---
obs0.192 17404 90.7 %-
Displacement parametersBiso mean: 26.8 Å2
Baniso -1Baniso -2Baniso -3
1--6.11 Å20 Å20 Å2
2--3.2 Å20 Å2
3---2.9 Å2
Refine analyzeLuzzati coordinate error obs: 0.32 Å / Luzzati d res low obs: 5 Å / Luzzati sigma a obs: 0.37 Å
Refinement stepCycle: LAST / Resolution: 2.15→18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2340 0 24 202 2566
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.01
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.63
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d29.2
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d0.85
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it2.921.5
X-RAY DIFFRACTIONx_mcangle_it4.582
X-RAY DIFFRACTIONx_scbond_it3.382
X-RAY DIFFRACTIONx_scangle_it4.652.5
LS refinement shellResolution: 2.15→2.2 Å / Total num. of bins used: 15
RfactorNum. reflection% reflection
Rfree0.205 --
Rwork0.188 3048 -
obs--97.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROPAR_SE.ODOR
X-RAY DIFFRACTION2XDICT_UND.PARXDICT_UND.TOP
Software
*PLUS
Name: X-PLOR / Version: 3.843 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg29.2
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg0.85

+
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