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- PDB-7qd2: Structure of the orange carotenoid protein from Planktothrix agar... -

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Basic information

Entry
Database: PDB / ID: 7qd2
TitleStructure of the orange carotenoid protein from Planktothrix agardhii binding canthaxanthin in the P21 space group
ComponentsOrange carotenoid-binding protein
KeywordsPHOTOSYNTHESIS / CAROTENOID-BINDING / PHOTOPROTECTION / CAROTENOID BINDING PROTEIN
Function / homology
Function and homology information


light absorption / phycobilisome / chloride ion binding
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 speciesPlanktothrix agardhii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsAndreeva, E.A. / Hartmann, E. / Schlichting, I. / Colletier, J.-P.
Funding support France, 4items
OrganizationGrant numberCountry
Agence Nationale de la Recherche (ANR)ANR-17-CE11-0018-01 France
Agence Nationale de la Recherche (ANR)ANR-2018-CE11-0005-02 France
Agence Nationale de la Recherche (ANR)ANR-10-INBS-05-02 France
Agence Nationale de la Recherche (ANR)ANR-17-EURE-0003 France
CitationJournal: Biochim Biophys Acta Bioenerg / Year: 2022
Title: Structure-function-dynamics relationships in the peculiar Planktothrix PCC7805 OCP1: Impact of his-tagging and carotenoid type.
Authors: Wilson, A. / Andreeva, E.A. / Nizinski, S.J. / Talbot, L. / Hartmann, E. / Schlichting, I. / Burdzinski, G. / Sliwa, M. / Kirilovsky, D. / Colletier, J.P.
History
DepositionNov 26, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 6, 2022Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2022Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.2Oct 5, 2022Group: Database references / Structure summary / Category: citation / struct / Item: _citation.journal_id_ISSN / _struct.title
Revision 1.3Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.4Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Orange carotenoid-binding protein
C: Orange carotenoid-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,0787
Polymers70,7052
Non-polymers1,3735
Water10,737596
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2920 Å2
ΔGint-1 kcal/mol
Surface area25860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.460, 65.940, 77.280
Angle α, β, γ (deg.)90.000, 102.262, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein Orange carotenoid-binding protein


Mass: 35352.434 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Planktothrix agardhii (bacteria) / Gene: PLAM_2315
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: A0A1J1JHR9
#2: Chemical ChemComp-45D / beta,beta-carotene-4,4'-dione / Isomer of Canthaxanthin


Mass: 564.840 Da / Num. of mol.: 2 / 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.: 2 / 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 596 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.32 Å3/Da / Density % sol: 46.98 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5 / Details: 0.1 M sodium acetate, pH 5 and 10-20% PEG4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.9998 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Aug 23, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9998 Å / Relative weight: 1
ReflectionResolution: 1.4→43.6 Å / Num. obs: 115206 / % possible obs: 93.9 % / Redundancy: 2.4 % / Biso Wilson estimate: 21.13 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.036 / Rpim(I) all: 0.028 / Rrim(I) all: 0.046 / Net I/σ(I): 11.47
Reflection shellResolution: 1.4→1.45 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.3938 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 11285 / CC1/2: 0.852 / Rpim(I) all: 0.3153 / Rrim(I) all: 0.5066 / % possible all: 92.54

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Processing

Software
NameVersionClassification
PHENIX1.19_4080refinement
PHASERphasing
XSCALEdata scaling
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3mg1

3mg1


Resolution: 1.4→43.6 Å / SU ML: 0.1706 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 24.5546
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2302 5753 5 %
Rwork0.2005 109294 -
obs0.2019 115047 93.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 30.31 Å2
Refinement stepCycle: LAST / Resolution: 1.4→43.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4781 0 100 596 5477
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00695355
X-RAY DIFFRACTIONf_angle_d0.94857327
X-RAY DIFFRACTIONf_chiral_restr0.0788797
X-RAY DIFFRACTIONf_plane_restr0.0091992
X-RAY DIFFRACTIONf_dihedral_angle_d16.94432016
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4-1.420.32771870.29293551X-RAY DIFFRACTION92.09
1.42-1.430.28191910.28323629X-RAY DIFFRACTION92.79
1.43-1.450.27631860.26683541X-RAY DIFFRACTION92.73
1.45-1.470.31771890.26563581X-RAY DIFFRACTION92.86
1.47-1.490.28581880.27313572X-RAY DIFFRACTION92.68
1.49-1.510.2861900.26363606X-RAY DIFFRACTION92.63
1.51-1.530.28681860.25943535X-RAY DIFFRACTION92.75
1.53-1.550.2991870.25363559X-RAY DIFFRACTION91.5
1.55-1.580.27061860.25033541X-RAY DIFFRACTION91.04
1.58-1.60.2651910.25213611X-RAY DIFFRACTION94.13
1.6-1.630.271910.2353639X-RAY DIFFRACTION94.22
1.63-1.660.27931930.2433669X-RAY DIFFRACTION94.66
1.66-1.690.27771930.2343659X-RAY DIFFRACTION94.57
1.69-1.730.24771920.23053651X-RAY DIFFRACTION94.15
1.73-1.760.26561930.23653672X-RAY DIFFRACTION94.75
1.76-1.80.27771930.22823661X-RAY DIFFRACTION94.9
1.8-1.850.27691920.23483653X-RAY DIFFRACTION94.77
1.85-1.90.25971940.22973678X-RAY DIFFRACTION94.55
1.9-1.960.25641920.22213653X-RAY DIFFRACTION94.54
1.96-2.020.23651920.21773643X-RAY DIFFRACTION94.16
2.02-2.090.22481910.21563643X-RAY DIFFRACTION93.56
2.09-2.170.2461880.21143566X-RAY DIFFRACTION92.01
2.18-2.270.24431950.20893702X-RAY DIFFRACTION94.75
2.27-2.390.24251940.20243678X-RAY DIFFRACTION95.58
2.39-2.540.22431970.20073752X-RAY DIFFRACTION95.62
2.54-2.740.23711960.20023734X-RAY DIFFRACTION96.23
2.74-3.020.22691970.19473738X-RAY DIFFRACTION96.02
3.02-3.450.23011980.18643764X-RAY DIFFRACTION96.19
3.45-4.350.18081970.15833731X-RAY DIFFRACTION94.83
4.35-43.60.19631940.17613682X-RAY DIFFRACTION91.85

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