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- PDB-7zsf: Structure of Orange Carotenoid Protein with canthaxanthin bound -

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Basic information

Entry
Database: PDB / ID: 7zsf
TitleStructure of Orange Carotenoid Protein with canthaxanthin bound
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: 1.36 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
A: Orange carotenoid-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,6275
Polymers35,8761
Non-polymers7514
Water6,990388
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 area14330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.569, 82.569, 87.365
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
11A-731-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Orange carotenoid-binding protein / OCP


Mass: 35875.887 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: ...Details: PFTIDSARGIFPNTLAADVVPATIARFSQLNAEDQLALIWFAYLEMGKTLTIAAPGAASMQLAENALKEIQAMGPLQQTQAMCDLANRADTPLCRTYASWSPNIKLGFWYRLGELMEQGFVAPIPAGYQLSANANAVLATIQGLESGQQITVLRNAVVDMGFTAGKDGKRIAEPVVPPQDTASRTKVSIEGVTNATVLNYMDNLNANDFDTLIELFTSDGALQPPFQRPIVGKENVLRFFREECQNLKLIPERGVTEPAEDGFTQIKVTGKVQTPWFGGNVGMNIAWRFLLNPEGKIFFVAIDLLASPKELLNF
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, 392 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
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 388 / 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: 2.5 Å3/Da / Density % sol: 50.89 %
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

Diffraction
IDMean temperature (K)Crystal-IDSerial crystal experiment
11001N
2501N
3501N
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONDiamond I0310.9796
SYNCHROTRONDiamond I2324.42801
SYNCHROTRONDiamond I2334.27532
Detector
TypeIDDetectorDate
DECTRIS EIGER2 XE 16M1PIXELJul 4, 2019
DECTRIS PILATUS 12M2PIXELJul 29, 2020
DECTRIS PILATUS 12M3PIXELJul 29, 2020
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-IDMonochromator
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray2Si 111
3SINGLE WAVELENGTHMx-ray3Si 111
Radiation wavelength
IDWavelength (Å)Relative weight
10.97961
24.428011
34.275321
Reflection

Entry-ID: 7ZSF

Resolution (Å)Num. obs% possible obs (%)Redundancy (%)Rmerge(I) obsRpim(I) allRrim(I) allΧ2Diffraction-IDNet I/σ(I)CC1/2
1.36-87.297425299.9719.90.0750.0250.0790.94117.1
2.8-72867498.321.90.1380.0270.14218.90.998
2.89-7278919821.70.1730.0350.177314.60.997
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2Diffraction-ID% possible all
1.36-1.419.93.5431.154380.5190.7793.480.881100
2.8-2.9512.80.3046.811880.9760.0820.316294.5
2.89-3.070.4134.8149520.9630.1110.429393.6

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Processing

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

4xb5


Resolution: 1.36→55.396 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.962 / WRfactor Rfree: 0.221 / WRfactor Rwork: 0.19 / SU B: 1.239 / SU ML: 0.049 / Average fsc free: 0.8958 / Average fsc work: 0.9037 / Cross valid method: THROUGHOUT / ESU R: 0.06 / ESU R Free: 0.062 / Details: Hydrogens have not been used
RfactorNum. reflection% reflectionSelection details
Rfree0.2179 3699 4.985 %RANDOM
Rwork0.189 70508 --
all0.19 ---
obs-74207 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: 25.954 Å2
Baniso -1Baniso -2Baniso -3
1-0.001 Å20 Å20 Å2
2--0.001 Å2-0 Å2
3----0.003 Å2
Refinement stepCycle: LAST / Resolution: 1.36→55.396 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2376 0 53 388 2817
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0122695
X-RAY DIFFRACTIONr_angle_refined_deg1.9571.6433690
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8225351
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.51421.538156
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.57915437
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.8141516
X-RAY DIFFRACTIONr_chiral_restr0.1170.2352
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.022124
X-RAY DIFFRACTIONr_nbd_refined0.2150.21329
X-RAY DIFFRACTIONr_nbtor_refined0.3140.21777
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2080.2295
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2750.266
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2050.225
X-RAY DIFFRACTIONr_mcbond_it2.1522.2541354
X-RAY DIFFRACTIONr_mcangle_it3.0963.3691721
X-RAY DIFFRACTIONr_scbond_it3.1732.4121341
X-RAY DIFFRACTIONr_scangle_it4.5933.5391969
X-RAY DIFFRACTIONr_lrange_it7.80732.8434304
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.36-1.3950.3222590.3225102X-RAY DIFFRACTION98.6385
1.395-1.4330.3322470.3055066X-RAY DIFFRACTION100
1.433-1.4750.2972690.2864875X-RAY DIFFRACTION100
1.475-1.520.2932450.2594767X-RAY DIFFRACTION100
1.52-1.570.2532600.2454598X-RAY DIFFRACTION100
1.57-1.6250.2852250.224498X-RAY DIFFRACTION100
1.625-1.6860.2451800.2164359X-RAY DIFFRACTION100
1.686-1.7550.2482320.2064141X-RAY DIFFRACTION100
1.755-1.8330.2282110.1994001X-RAY DIFFRACTION100
1.833-1.9230.2052110.1893793X-RAY DIFFRACTION100
1.923-2.0270.1972170.1993616X-RAY DIFFRACTION100
2.027-2.1490.2311940.1973461X-RAY DIFFRACTION100
2.149-2.2980.2341980.1843221X-RAY DIFFRACTION100
2.298-2.4820.2051560.1883025X-RAY DIFFRACTION100
2.482-2.7180.2041450.182810X-RAY DIFFRACTION100
2.718-3.0390.2471210.1782559X-RAY DIFFRACTION100
3.039-3.5080.2031090.1662268X-RAY DIFFRACTION100
3.508-4.2950.1551040.1461934X-RAY DIFFRACTION100
4.295-6.0670.185810.1641516X-RAY DIFFRACTION100
6.067-55.30.281350.211898X-RAY DIFFRACTION99.7861

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