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- PDB-7qd0: Structure of the orange carotenoid protein from Planktothrix agar... -

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Basic information

Entry
Database: PDB / ID: 7qd0
TitleStructure of the orange carotenoid protein from Planktothrix agardhii binding echinenone in the C2 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
ACETATE ION / ARGININE / beta,beta-caroten-4-one / Orange carotenoid-binding protein
Similarity search - Component
Biological speciesPlanktothrix agardhii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 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 25, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,65710
Polymers35,3521
Non-polymers1,3059
Water4,666259
1
A: Orange carotenoid-binding protein
hetero molecules

A: Orange carotenoid-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,31420
Polymers70,7052
Non-polymers2,60918
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area6060 Å2
ΔGint-5 kcal/mol
Surface area24730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.400, 64.870, 61.690
Angle α, β, γ (deg.)90.000, 117.911, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Components on special symmetry positions
IDModelComponents
11A-514-

HOH

21A-604-

HOH

31A-687-

HOH

41A-735-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Orange carotenoid-binding protein


Mass: 35352.434 Da / Num. of mol.: 1
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

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Non-polymers , 5 types, 268 molecules

#2: Chemical ChemComp-ARG / ARGININE


Type: L-peptide linking / Mass: 175.209 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H15N4O2
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical ChemComp-ECH / beta,beta-caroten-4-one / echinenone


Mass: 550.856 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C40H54O / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 259 / 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: 2.12 Å3/Da / Density % sol: 41.93 %
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: ESRF / Beamline: ID29 / Wavelength: 0.9537 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 2, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.7→32.44 Å / Num. obs: 30918 / % possible obs: 98.61 % / Redundancy: 3.3 % / Biso Wilson estimate: 25.58 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.046 / Rpim(I) all: 0.03 / Rrim(I) all: 0.055 / Net I/σ(I): 13.78
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.7233 / Mean I/σ(I) obs: 1.85 / Num. unique obs: 3107 / CC1/2: 0.843 / Rpim(I) all: 0.3882 / Rrim(I) all: 0.7233 / % possible all: 99.42

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Processing

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

3mg1


Resolution: 1.7→32.44 Å / SU ML: 0.2059 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26.2509
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2228 1545 5.01 %
Rwork0.1776 29310 -
obs0.1798 30855 98.62 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 34.32 Å2
Refinement stepCycle: LAST / Resolution: 1.7→32.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2387 0 91 259 2737
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00742854
X-RAY DIFFRACTIONf_angle_d1.34023903
X-RAY DIFFRACTIONf_chiral_restr0.1966423
X-RAY DIFFRACTIONf_plane_restr0.0087531
X-RAY DIFFRACTIONf_dihedral_angle_d16.1116427
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.750.35341410.30232677X-RAY DIFFRACTION99.47
1.75-1.820.28991400.26192646X-RAY DIFFRACTION98.72
1.82-1.890.27931400.23072655X-RAY DIFFRACTION99.22
1.89-1.980.29091390.22182647X-RAY DIFFRACTION98.69
1.98-2.080.27141430.20062707X-RAY DIFFRACTION99.06
2.08-2.210.22571400.1772651X-RAY DIFFRACTION99.08
2.21-2.380.21131400.17582669X-RAY DIFFRACTION99.05
2.38-2.620.24611400.19692641X-RAY DIFFRACTION97.72
2.62-30.25931390.1862640X-RAY DIFFRACTION98.23
3-3.780.22281390.15712648X-RAY DIFFRACTION96.91
3.78-32.440.1681440.1522729X-RAY DIFFRACTION98.73

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