[English] 日本語
Yorodumi
- PDB-7zsi: Structure of Orange Carotenoid Protein with canthaxanthin bound a... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7zsi
TitleStructure of Orange Carotenoid Protein with canthaxanthin bound after 5 minutes of illumination
ComponentsOrange carotenoid-binding protein
KeywordsPHOTOSYNTHESIS / photoreceptor / carotenoid
Function / homology
Function and homology information


light absorption / phycobilisome / chloride ion binding / plasma membrane-derived thylakoid membrane / photoreceptor activity
Similarity search - Function
Orange carotenoid-binding protein, N-terminal / Orange carotenoid-binding protein, N-terminal domain superfamily / Orange carotenoid protein, N-terminal / Orange carotenoid protein (OCP) N-terminal domain profile. / Nuclear transport factor 2 domain / Nuclear transport factor 2 (NTF2) domain / NTF2-like domain superfamily
Similarity search - Domain/homology
beta,beta-carotene-4,4'-dione / ACETATE ION / Orange carotenoid-binding protein
Similarity search - Component
Biological speciesSynechocystis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.399 Å
AuthorsChukhutsina, V.U. / Baxter, J.M. / Fadini, A. / Morgan, R.M. / Pope, M.A. / Maghlaoui, K. / Orr, C. / Wagner, A. / van Thor, J.J.
Funding supportEuropean Union, United Kingdom, 5items
OrganizationGrant numberCountry
European Molecular Biology Organization (EMBO)EMBO ALTF 244-2017European Union
H2020 Marie Curie Actions of the European Commission839389European Union
Leverhulme TrustRPG-2018-372 United Kingdom
Biotechnology and Biological Sciences Research Council (BBSRC)BB/D524840/1 United Kingdom
Wellcome Trust202926/Z/16/Z United Kingdom
CitationJournal: Nat Commun / Year: 2022
Title: Light activation of Orange Carotenoid Protein reveals bicycle-pedal single-bond isomerization.
Authors: Chukhutsina, V.U. / Baxter, J.M. / Fadini, A. / Morgan, R.M. / Pope, M.A. / Maghlaoui, K. / Orr, C.M. / Wagner, A. / van Thor, J.J.
History
DepositionMay 6, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 9, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
1: Orange carotenoid-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,6275
Polymers35,8761
Non-polymers7514
Water7,206400
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area630 Å2
ΔGint-14 kcal/mol
Surface area14580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.780, 82.780, 87.604
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
111-720-

HOH

-
Components

-
Protein , 1 types, 1 molecules 1

#1: Protein Orange carotenoid-binding protein / OCP


Mass: 35875.887 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Synechocystis (bacteria) / Strain: PCC 6803 / Kazusa / Gene: slr1963 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): gold / References: UniProt: P74102

-
Non-polymers , 5 types, 404 molecules

#2: Chemical ChemComp-45D / beta,beta-carotene-4,4'-dione / Isomer of Canthaxanthin


Mass: 564.840 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C40H52O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 400 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.53 Å3/Da / Density % sol: 51.41 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: 100 mM sodium acetate pH 4.5, 10 % poly-ethylene glycol 20,000, 3 % glycerol

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Jul 4, 2019
RadiationMonochromator: DIAMOND BEAMLINE I03 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.399→55.542 Å / Num. obs: 68765 / % possible obs: 100 % / Redundancy: 19.8 % / Rmerge(I) obs: 0.133 / Rpim(I) all: 0.044 / Rrim(I) all: 0.14 / Net I/σ(I): 14.4
Reflection shellResolution: 1.4→1.44 Å / Rmerge(I) obs: 9.9 / Num. unique obs: 5049 / Rpim(I) all: 3.645 / Rrim(I) all: 11.51

-
Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
DIALSdata reduction
DIALSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4XB5

4xb5


Resolution: 1.399→55.542 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.963 / WRfactor Rfree: 0.21 / WRfactor Rwork: 0.197 / SU B: 2.08 / SU ML: 0.079 / Average fsc free: 0.9106 / Average fsc work: 0.9181 / Cross valid method: THROUGHOUT / ESU R: 0.1 / ESU R Free: 0.086 / Details: Hydrogens have not been used
RfactorNum. reflection% reflection
Rfree0.2048 3410 4.963 %
Rwork0.1912 65300 -
all0.192 --
obs-68710 99.897 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 25.71 Å2
Baniso -1Baniso -2Baniso -3
1-0.009 Å20.004 Å20 Å2
2--0.009 Å2-0 Å2
3----0.029 Å2
Refinement stepCycle: LAST / Resolution: 1.399→55.542 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2411 0 53 400 2864
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0125024
X-RAY DIFFRACTIONr_angle_refined_deg1.7381.6436838
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8215626
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.54821.549284
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.1915792
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.0071526
X-RAY DIFFRACTIONr_chiral_restr0.1040.2662
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.023850
X-RAY DIFFRACTIONr_nbd_refined0.2120.21171
X-RAY DIFFRACTIONr_nbtor_refined0.3110.21735
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2690.2259
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2290.243
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.3650.230
X-RAY DIFFRACTIONr_mcbond_it2.0722.1992512
X-RAY DIFFRACTIONr_mcangle_it3.0993.2873134
X-RAY DIFFRACTIONr_scbond_it2.7742.3932512
X-RAY DIFFRACTIONr_scangle_it4.0513.4953704
X-RAY DIFFRACTIONr_lrange_it7.24526.8895041
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.399-1.4360.3622400.3274768X-RAY DIFFRACTION99.3848
1.436-1.4750.3212770.34626X-RAY DIFFRACTION99.9796
1.475-1.5180.2722220.2724511X-RAY DIFFRACTION99.9789
1.518-1.5640.2972390.2494444X-RAY DIFFRACTION99.9573
1.564-1.6160.2731800.2294305X-RAY DIFFRACTION99.9777
1.616-1.6720.232370.2184121X-RAY DIFFRACTION100
1.672-1.7350.2562130.2033972X-RAY DIFFRACTION99.9045
1.735-1.8060.1931860.1943861X-RAY DIFFRACTION99.9506
1.806-1.8870.2161750.1983748X-RAY DIFFRACTION99.9745
1.887-1.9790.2191760.1983537X-RAY DIFFRACTION100
1.979-2.0860.2311750.2063377X-RAY DIFFRACTION100
2.086-2.2120.211690.23175X-RAY DIFFRACTION100
2.212-2.3650.1991540.1933040X-RAY DIFFRACTION100
2.365-2.5540.1991670.182767X-RAY DIFFRACTION100
2.554-2.7970.1681420.1732597X-RAY DIFFRACTION100
2.797-3.1270.1971280.1762343X-RAY DIFFRACTION100
3.127-3.610.175970.1622113X-RAY DIFFRACTION100
3.61-4.420.1531040.1541770X-RAY DIFFRACTION100
4.42-6.2420.203810.1841414X-RAY DIFFRACTION100
6.242-55.540.223480.208811X-RAY DIFFRACTION99.3064

+
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