[English] 日本語
Yorodumi
- PDB-1n8v: Chemosensory Protein in complex with bromo-dodecanol -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1n8v
TitleChemosensory Protein in complex with bromo-dodecanol
Componentschemosensory protein
KeywordsLIPID BINDING PROTEIN
Function / homologyAntennal chemosensory protein a6 / Insect odorant-binding protein A10/Ejaculatory bulb-specific protein 3 / Insect odorant-binding protein A10/Ejaculatory bulb-specific protein 3 / Insect odorant-binding protein A10/Ejaculatory bulb-specific protein 3 superfamily / Insect pheromone-binding family, A10/OS-D / Orthogonal Bundle / Mainly Alpha / BROMO-DODECANOL / Chemosensory protein
Function and homology information
Biological speciesMamestra brassicae (cabbage moth)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.39 Å
AuthorsCampanacci, V. / Lartigue, A. / Hallberg, B.M. / Jones, T.A. / Giudici-Orticoni, M.T. / Tegoni, M. / Cambillau, C.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2003
Title: Moth chemosensory protein exhibits drastic conformational changes and cooperativity on ligand binding.
Authors: Campanacci, V. / Lartigue, A. / Hallberg, B.M. / Jones, T.A. / Giudici-Orticoni, M.T. / Tegoni, M. / Cambillau, C.
History
DepositionNov 21, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 1, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 1, 2017Group: Structure summary

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: chemosensory protein
B: chemosensory protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,7818
Polymers26,1902
Non-polymers1,5916
Water7,296405
1
A: chemosensory protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,8914
Polymers13,0951
Non-polymers7963
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: chemosensory protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,8914
Polymers13,0951
Non-polymers7963
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)33.460, 54.180, 56.380
Angle α, β, γ (deg.)90.00, 93.88, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein chemosensory protein


Mass: 13094.840 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mamestra brassicae (cabbage moth) / Plasmid: PET-22B+ / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21-DE3 / References: UniProt: Q9NG96
#2: Chemical
ChemComp-BDD / BROMO-DODECANOL


Mass: 265.230 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C12H25BrO
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 405 / 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: 1.69 Å3/Da / Density % sol: 26.58 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 34% MPEG 2000, 0.1M Na cacodylate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
134 %mPEG200011
20.1 Msodium cacodylate11pH6.5

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9197 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 5, 2000
RadiationMonochromator: Mirrors / Protocol: SAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9197 Å / Relative weight: 1
ReflectionResolution: 1.39→55 Å / Num. all: 38354 / Num. obs: 38354 / % possible obs: 95.7 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 2.9 % / Rmerge(I) obs: 0.054 / Net I/σ(I): 5.7
Reflection shellResolution: 1.39→1.44 Å / Rmerge(I) obs: 0.247 / Mean I/σ(I) obs: 2.6 / % possible all: 87
Reflection
*PLUS
Lowest resolution: 55 Å

-
Processing

Software
NameVersionClassification
DENZOdata reduction
SCALAdata scaling
SOLVEphasing
REFMAC5refinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: SAD / Resolution: 1.39→55 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.946 / SU B: 1.536 / SU ML: 0.062 / TLS residual ADP flag: UNVERIFIED / Cross valid method: THROUGHOUT / σ(F): 1 / ESU R: 0.071 / ESU R Free: 0.07 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20178 1544 4 %RANDOM
Rwork0.18002 ---
all0.1809 36789 --
obs0.1809 36789 95.64 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 14.18 Å2
Baniso -1Baniso -2Baniso -3
1--0.06 Å20 Å20.34 Å2
2--0.31 Å20 Å2
3----0.21 Å2
Refinement stepCycle: LAST / Resolution: 1.39→55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1668 0 84 405 2157
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0211773
X-RAY DIFFRACTIONr_bond_other_d0.0110.021640
X-RAY DIFFRACTIONr_angle_refined_deg1.3731.9922352
X-RAY DIFFRACTIONr_angle_other_deg1.17133866
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.2993202
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.06315337
X-RAY DIFFRACTIONr_chiral_restr0.0890.2240
X-RAY DIFFRACTIONr_gen_planes_refined0.0250.021877
X-RAY DIFFRACTIONr_gen_planes_other0.0730.02322
X-RAY DIFFRACTIONr_nbd_refined0.2670.3469
X-RAY DIFFRACTIONr_nbd_other0.2150.31542
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2130.5239
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.3210.54
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.0920.39
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1870.330
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2150.537
X-RAY DIFFRACTIONr_symmetry_hbond_other0.040.51
X-RAY DIFFRACTIONr_mcbond_it0.7711.51014
X-RAY DIFFRACTIONr_mcangle_it1.43621622
X-RAY DIFFRACTIONr_scbond_it2.5663759
X-RAY DIFFRACTIONr_scangle_it3.8434.5730
LS refinement shellResolution: 1.39→1.431 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.249 73
Rwork0.221 2331
Refinement TLS params.Method: refined / Origin x: 6.978 Å / Origin y: 26.809 Å / Origin z: 13.829 Å
111213212223313233
T0.0006 Å2-0.0008 Å20.0021 Å2-0.0059 Å2-0.0006 Å2--0.009 Å2
L0.1322 °20.0181 °20.0738 °2-0.085 °2-0.0319 °2--0.6025 °2
S-0.0207 Å °-0.0011 Å °-0.0232 Å °-0.0007 Å °-0.0102 Å °-0.0119 Å °-0.0028 Å °-0.0156 Å °0.0309 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA3 - 1033 - 103
2X-RAY DIFFRACTION1BB1 - 1031 - 103
3X-RAY DIFFRACTION1A - BC - H501 - 5131
Software
*PLUS
Version: 5 / Classification: refinement
Refinement
*PLUS
Rfactor Rfree: 0.2 / Rfactor Rwork: 0.18
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.011
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.37
LS refinement shell
*PLUS
Lowest resolution: 1.44 Å

+
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://pdbjlvh1.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