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

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Basic information

Entry
Database: PDB / ID: 7zsj
TitleStructure of Orange Carotenoid Protein with canthaxanthin bound after 10 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: 1.41 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
Water7,188399
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 area14380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.260, 82.260, 86.250
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
111-678-

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, 403 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.: 399 / 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: 2.47 Å3/Da / Density % sol: 50.26 %
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: I03 / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Jul 4, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.37→29.86 Å / Num. obs: 71802 / % possible obs: 100 % / Redundancy: 19.2 % / Rmerge(I) obs: 0.046 / Rpim(I) all: 0.015 / Rrim(I) all: 0.048 / Net I/σ(I): 24.6
Reflection shellResolution: 1.37→1.41 Å / Rmerge(I) obs: 2.561 / Num. unique obs: 5231 / Rpim(I) all: 0.966 / Rrim(I) all: 2.74

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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: 1.41→28.767 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.957 / WRfactor Rfree: 0.239 / WRfactor Rwork: 0.196 / SU B: 2.922 / SU ML: 0.108 / Average fsc free: 0.8525 / Average fsc work: 0.8635 / Cross valid method: THROUGHOUT / ESU R: 0.105 / ESU R Free: 0.1 / Details: Hydrogens have not been used
RfactorNum. reflection% reflection
Rfree0.2301 3207 4.911 %
Rwork0.1908 62099 -
all0.193 --
obs-65306 99.884 %
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: 31.033 Å2
Baniso -1Baniso -2Baniso -3
1-0.068 Å20.034 Å20 Å2
2--0.068 Å2-0 Å2
3----0.22 Å2
Refinement stepCycle: LAST / Resolution: 1.41→28.767 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2411 0 53 399 2863
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0125024
X-RAY DIFFRACTIONr_angle_refined_deg1.7671.6436838
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8835626
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.19221.549284
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.49315792
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.3191526
X-RAY DIFFRACTIONr_chiral_restr0.0980.2662
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.023850
X-RAY DIFFRACTIONr_nbd_refined0.2140.21339
X-RAY DIFFRACTIONr_nbtor_refined0.3170.21770
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2140.2291
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2070.258
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2910.238
X-RAY DIFFRACTIONr_mcbond_it2.132.7542512
X-RAY DIFFRACTIONr_mcangle_it3.0924.1213134
X-RAY DIFFRACTIONr_scbond_it2.8472.9462512
X-RAY DIFFRACTIONr_scangle_it3.9874.3263704
X-RAY DIFFRACTIONr_lrange_it7.54533.9145267
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.41-1.4470.3952300.374551X-RAY DIFFRACTION99.833
1.447-1.4860.3452590.3314389X-RAY DIFFRACTION99.914
1.486-1.5290.3162350.3084315X-RAY DIFFRACTION99.8683
1.529-1.5760.3161730.2764208X-RAY DIFFRACTION99.9772
1.576-1.6280.2751880.2554073X-RAY DIFFRACTION99.9062
1.628-1.6850.2642060.2453941X-RAY DIFFRACTION99.9036
1.685-1.7490.2761500.2223867X-RAY DIFFRACTION99.8509
1.749-1.820.2632120.2173619X-RAY DIFFRACTION99.9218
1.82-1.9010.2251990.1963496X-RAY DIFFRACTION100
1.901-1.9940.2531680.1963366X-RAY DIFFRACTION99.8869
1.994-2.1020.2441590.1933234X-RAY DIFFRACTION99.9705
2.102-2.2290.2281790.1843017X-RAY DIFFRACTION100
2.229-2.3830.2051380.1832879X-RAY DIFFRACTION100
2.383-2.5730.2151330.1812667X-RAY DIFFRACTION100
2.573-2.8190.2411340.1782455X-RAY DIFFRACTION99.9228
2.819-3.1510.2251210.1732250X-RAY DIFFRACTION100
3.151-3.6380.1991080.1661978X-RAY DIFFRACTION99.9042
3.638-4.4530.187870.1581698X-RAY DIFFRACTION100
4.453-6.290.251800.1781332X-RAY DIFFRACTION100
6.29-28.760.221480.223764X-RAY DIFFRACTION97.8313

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