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- PDB-7zsh: Structure of Orange Carotenoid Protein with canthaxanthin bound a... -

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Basic information

Entry
Database: PDB / ID: 7zsh
TitleStructure of Orange Carotenoid Protein with canthaxanthin bound after 2 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 (NTF2) domain / Nuclear transport factor 2 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: 1.42 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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 area14450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.482, 82.482, 87.219
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
111-676-

HOH

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Components

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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

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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

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Details

Has ligand of interestY

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.52 Å3/Da / Density % sol: 51.2 %
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

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Jun 24, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.42→29.09 Å / Num. obs: 65092 / % possible obs: 100 % / Redundancy: 19.5 % / Rmerge(I) obs: 0.067 / Rpim(I) all: 0.021 / Rrim(I) all: 0.069 / Net I/σ(I): 19.1
Reflection shellResolution: 1.42→1.46 Å / Rmerge(I) obs: 2.79 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 4775 / Rpim(I) all: 0.94 / Rrim(I) all: 2.871

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Processing

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

4xb5


Resolution: 1.42→29.09 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.962 / WRfactor Rfree: 0.215 / WRfactor Rwork: 0.185 / SU B: 2.455 / SU ML: 0.093 / Average fsc free: 0.899 / Average fsc work: 0.9047 / Cross valid method: THROUGHOUT / ESU R: 0.107 / ESU R Free: 0.094 / Details: Hydrogens have not been used
RfactorNum. reflection% reflection
Rfree0.2148 3272 5.031 %
Rwork0.1924 61770 -
all0.194 --
obs-65042 99.937 %
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: 28.202 Å2
Baniso -1Baniso -2Baniso -3
1-0.013 Å20.006 Å20 Å2
2--0.013 Å20 Å2
3----0.041 Å2
Refinement stepCycle: LAST / Resolution: 1.42→29.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2411 0 53 400 2864
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0125024
X-RAY DIFFRACTIONr_angle_refined_deg1.651.6436838
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8835626
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.81421.549284
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.08315792
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.9341526
X-RAY DIFFRACTIONr_chiral_restr0.0990.2662
X-RAY DIFFRACTIONr_gen_planes_refined0.010.023850
X-RAY DIFFRACTIONr_nbd_refined0.2140.21247
X-RAY DIFFRACTIONr_nbtor_refined0.3140.21753
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2580.2281
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2320.249
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.3490.231
X-RAY DIFFRACTIONr_mcbond_it1.9342.4812512
X-RAY DIFFRACTIONr_mcangle_it2.953.7113134
X-RAY DIFFRACTIONr_scbond_it2.5622.6512512
X-RAY DIFFRACTIONr_scangle_it3.7223.8923704
X-RAY DIFFRACTIONr_lrange_it7.17130.2695153
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.42-1.4570.3082240.3254531X-RAY DIFFRACTION99.7692
1.457-1.4970.3022480.2924406X-RAY DIFFRACTION99.9785
1.497-1.540.3142040.2764297X-RAY DIFFRACTION99.9556
1.54-1.5880.32480.264146X-RAY DIFFRACTION99.9318
1.588-1.640.241880.2314048X-RAY DIFFRACTION99.9764
1.64-1.6970.2212160.2293906X-RAY DIFFRACTION99.9757
1.697-1.7610.2581700.2223836X-RAY DIFFRACTION100
1.761-1.8330.2541650.2123669X-RAY DIFFRACTION100
1.833-1.9150.2552200.1983455X-RAY DIFFRACTION99.9456
1.915-2.0080.2321910.2033337X-RAY DIFFRACTION100
2.008-2.1160.2231890.1973180X-RAY DIFFRACTION100
2.116-2.2450.2321720.1982981X-RAY DIFFRACTION100
2.245-2.40.2011420.1892862X-RAY DIFFRACTION100
2.4-2.5920.2111250.1872675X-RAY DIFFRACTION100
2.592-2.8390.221380.1852451X-RAY DIFFRACTION100
2.839-3.1740.1911060.1692248X-RAY DIFFRACTION100
3.174-3.6640.1741060.1661963X-RAY DIFFRACTION100
3.664-4.4850.178950.1561685X-RAY DIFFRACTION100
4.485-6.3350.19750.1861336X-RAY DIFFRACTION100
6.335-29.090.248500.215758X-RAY DIFFRACTION98.0583

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