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- PDB-7qd1: Structure of the orange carotenoid protein from Planktothrix agar... -

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Basic information

Entry
Database: PDB / ID: 7qd1
TitleStructure of the orange carotenoid protein from Planktothrix agardhii binding echinenone 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 domain / Nuclear transport factor 2 (NTF2) domain / NTF2-like domain superfamily
Similarity search - Domain/homology
beta,beta-caroten-4-one / Orange carotenoid-binding protein
Similarity search - Component
Biological speciesPlanktothrix agardhii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.71 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 1.2Jan 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
C: Orange carotenoid-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,8074
Polymers70,7052
Non-polymers1,1022
Water12,683704
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)63.363, 65.902, 77.372
Angle α, β, γ (deg.)90.000, 102.354, 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-ECH / beta,beta-caroten-4-one / echinenone


Mass: 550.856 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C40H54O / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 704 / Source method: isolated from a natural source / Formula: H2O
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: 2.31 Å3/Da / Density % sol: 46.64 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5 / Details: 0.2 M Bis-Tris pH 5.5, 20%-25% PEG 3550

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9786 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 28, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 1.71→75.58 Å / Num. obs: 60669 / % possible obs: 90 % / Redundancy: 3.5 % / Biso Wilson estimate: 26.66 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.063 / Rpim(I) all: 0.038 / Rrim(I) all: 0.074 / Net I/σ(I): 11.16
Reflection shellResolution: 1.71→1.75 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.685 / Mean I/σ(I) obs: 1.21 / Num. unique obs: 2735 / CC1/2: 0.426 / Rpim(I) all: 0.547 / Rrim(I) all: 0.877 / % possible all: 54.8

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Processing

Software
NameVersionClassification
PHENIX1.19_4080refinement
PHASER1.19_4080phasing
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3mg1

3mg1


Resolution: 1.71→41.71 Å / SU ML: 0.2488 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 24.9268
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2159 3015 4.97 %
Rwork0.1806 57643 -
obs0.1824 60658 90.03 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 32.37 Å2
Refinement stepCycle: LAST / Resolution: 1.71→41.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4810 0 82 704 5596
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00495315
X-RAY DIFFRACTIONf_angle_d1.33967276
X-RAY DIFFRACTIONf_chiral_restr0.1562803
X-RAY DIFFRACTIONf_plane_restr0.0073990
X-RAY DIFFRACTIONf_dihedral_angle_d18.73141991
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.71-1.740.5757810.47711519X-RAY DIFFRACTION52.68
1.74-1.770.47291030.42161705X-RAY DIFFRACTION59.38
1.77-1.80.4869970.37931817X-RAY DIFFRACTION63.29
1.8-1.830.3339930.32892027X-RAY DIFFRACTION69.28
1.83-1.860.31651040.29162260X-RAY DIFFRACTION77.1
1.86-1.90.30841240.26282458X-RAY DIFFRACTION85.47
1.9-1.940.27151520.22512741X-RAY DIFFRACTION94.36
1.94-1.990.25381410.21952881X-RAY DIFFRACTION98.63
1.99-2.040.27491410.22022883X-RAY DIFFRACTION98.95
2.04-2.090.2521580.22112829X-RAY DIFFRACTION99.2
2.09-2.150.23381620.2022865X-RAY DIFFRACTION98.99
2.15-2.220.24771520.19122850X-RAY DIFFRACTION98.52
2.22-2.30.22561570.18882864X-RAY DIFFRACTION98.47
2.3-2.40.23141600.18352868X-RAY DIFFRACTION99.02
2.4-2.50.24871530.19262870X-RAY DIFFRACTION98.98
2.5-2.640.21821480.18782893X-RAY DIFFRACTION98.83
2.64-2.80.21671660.18942815X-RAY DIFFRACTION97.45
2.8-3.020.21321580.18472867X-RAY DIFFRACTION98.95
3.02-3.320.22861320.17072929X-RAY DIFFRACTION98.97
3.32-3.80.17471440.14242869X-RAY DIFFRACTION97.73
3.8-4.790.15841480.13312920X-RAY DIFFRACTION98.81
4.79-41.710.17041410.15912913X-RAY DIFFRACTION96.65

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