[English] 日本語
Yorodumi
- PDB-6q53: CRYSTAL STRUCTURE OF THE LIGHT-HARVESTING COMPLEX II (B800-850) F... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6q53
TitleCRYSTAL STRUCTURE OF THE LIGHT-HARVESTING COMPLEX II (B800-850) FROM Ectothiorhodospira haloalkaliphila
Components
  • Light-harvesting protein B:800-850 subunit beta
  • light-harvesting protein subunit alpha
KeywordsPHOTOSYNTHESIS / LIGHT HARVESTING COMPLEX / BACTERIOCHLOROPHYLL / DEXTER ENERGY TRANSFER / FOERSTER EXCITON TRANSFER MECHANISM / MEMBRANE PROTEIN
Function / homology
Function and homology information


plasma membrane light-harvesting complex / bacteriochlorophyll binding / : / photosynthesis, light reaction / metal ion binding / plasma membrane
Similarity search - Function
Antenna complex, alpha/beta subunit / Light-harvesting protein B beta chain / Antenna complex, beta domain superfamily / Antenna complex alpha/beta subunit / Light-harvesting complex
Similarity search - Domain/homology
BACTERIOCHLOROPHYLL A / UNDECYLAMINE-N,N-DIMETHYL-N-OXIDE / LYCOPENE / Light-harvesting protein B:800-850 subunit beta
Similarity search - Component
Biological speciesEctothiorhodospira haloalkaliphila (bacteria)
Halorhodospira halochloris str. A (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.701 Å
AuthorsGabdulkhakov, A.G.
Funding support Russian Federation, 1items
OrganizationGrant numberCountry
program of the Presidium of the Russian Academy of Sciences Molecular and Cell Biology and Postgenomic Technologies Russian Federation
CitationJournal: J.Phys.Chem.B / Year: 2019
Title: Controlling Photosynthetic Excitons by Selective Pigment Photooxidation.
Authors: Leiger, K. / Linnanto, J.M. / Ratsep, M. / Timpmann, K. / Ashikhmin, A.A. / Moskalenko, A.A. / Fufina, T.Y. / Gabdulkhakov, A.G. / Freiberg, A.
History
DepositionDec 7, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 16, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: light-harvesting protein subunit alpha
B: Light-harvesting protein B:800-850 subunit beta
D: light-harvesting protein subunit alpha
E: Light-harvesting protein B:800-850 subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,08315
Polymers24,8944
Non-polymers7,18911
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18340 Å2
ΔGint-123 kcal/mol
Surface area12890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)177.240, 177.240, 177.240
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number207
Space group name H-MP432

-
Components

#1: Protein light-harvesting protein subunit alpha


Mass: 7139.147 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ectothiorhodospira haloalkaliphila (bacteria)
Production host: Ectothiorhodospira haloalkaliphila (bacteria)
#2: Protein/peptide Light-harvesting protein B:800-850 subunit beta


Mass: 5308.088 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Halorhodospira halochloris str. A (bacteria)
Gene: M911_15650
Production host: Ectothiorhodospira haloalkaliphila (bacteria)
References: UniProt: W8L932
#3: Chemical
ChemComp-BCL / BACTERIOCHLOROPHYLL A


Mass: 911.504 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C55H74MgN4O6
#4: Chemical ChemComp-LYC / LYCOPENE


Mass: 536.873 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C40H56
#5: Chemical ChemComp-DET / UNDECYLAMINE-N,N-DIMETHYL-N-OXIDE


Mass: 215.375 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C13H29NO

-
Experimental details

-
Experiment

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

-
Sample preparation

Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7.8
Details: 3.5% 1,2,3-heptanetriol, 2% dioxane, 0.05% LDAO and 1 M potassium phosphate,

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.97989 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jun 21, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97989 Å / Relative weight: 1
ReflectionResolution: 3.6→100 Å / Num. obs: 11486 / % possible obs: 99.9 % / Redundancy: 18.6 % / Net I/σ(I): 10.8
Reflection shellResolution: 3.6→3.7 Å

-
Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1LGH

1lgh


Resolution: 3.701→29.959 Å / SU ML: 0.47 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 28.11
RfactorNum. reflection% reflection
Rfree0.2769 534 5 %
Rwork0.2403 --
obs0.2418 10670 99.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.701→29.959 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1649 0 499 0 2148
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0152264
X-RAY DIFFRACTIONf_angle_d1.9873164
X-RAY DIFFRACTIONf_dihedral_angle_d16.7881150
X-RAY DIFFRACTIONf_chiral_restr0.149305
X-RAY DIFFRACTIONf_plane_restr0.011388
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.7005-4.07210.30771290.24692452X-RAY DIFFRACTION100
4.0721-4.65950.2481320.21482492X-RAY DIFFRACTION100
4.6595-5.86320.26591320.23082518X-RAY DIFFRACTION100
5.8632-29.960.28941410.25752674X-RAY DIFFRACTION100

+
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