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

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Basic information

Entry
Database: PDB / ID: 7qcz
TitleStructure of the orange carotenoid protein from Planktothrix agardhii binding canthaxanthin 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
beta,beta-carotene-4,4'-dione / Orange carotenoid-binding protein
Similarity search - Component
Biological speciesPlanktothrix agardhii (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.85 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

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Assembly

Deposited unit
A: Orange carotenoid-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,9172
Polymers35,3521
Non-polymers5651
Water7,692427
1
A: Orange carotenoid-binding protein
hetero molecules

A: Orange carotenoid-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,8354
Polymers70,7052
Non-polymers1,1302
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area3410 Å2
ΔGint-2 kcal/mol
Surface area25270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.010, 67.500, 61.940
Angle α, β, γ (deg.)90.000, 117.821, 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-600-

HOH

21A-652-

HOH

31A-866-

HOH

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Components

#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
#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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 427 / 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: 2.14 Å3/Da / Density % sol: 42.64 %
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: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Oct 23, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.85→19.23 Å / Num. obs: 23806 / % possible obs: 92.94 % / Redundancy: 2.4 % / Biso Wilson estimate: 26.48 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.052 / Rpim(I) all: 0.04 / Rrim(I) all: 0.066 / Net I/σ(I): 11.96
Reflection shellResolution: 1.85→1.92 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.5813 / Mean I/σ(I) obs: 1.83 / Num. unique obs: 2022 / CC1/2: 0.675 / Rpim(I) all: 0.4513 / Rrim(I) all: 0.7392 / % possible all: 79.92

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Processing

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

3mg1


Resolution: 1.85→18.26 Å / SU ML: 0.277 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 26.5786
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.245 1190 5 %
Rwork0.1752 22613 -
obs0.1787 23803 92.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 30.34 Å2
Refinement stepCycle: LAST / Resolution: 1.85→18.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2405 0 42 427 2874
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00462652
X-RAY DIFFRACTIONf_angle_d0.85433635
X-RAY DIFFRACTIONf_chiral_restr0.0491399
X-RAY DIFFRACTIONf_plane_restr0.0091492
X-RAY DIFFRACTIONf_dihedral_angle_d8.5402383
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.85-1.920.41041110.36882114X-RAY DIFFRACTION78.32
1.92-2.010.31461320.23832499X-RAY DIFFRACTION93.1
2.01-2.110.26961340.2152561X-RAY DIFFRACTION93.84
2.11-2.250.26911330.18472516X-RAY DIFFRACTION93.97
2.25-2.420.26881360.1872581X-RAY DIFFRACTION94.74
2.42-2.660.25411350.19472567X-RAY DIFFRACTION95.48
2.66-3.050.25711360.17932590X-RAY DIFFRACTION95.92
3.05-3.830.24511370.14952609X-RAY DIFFRACTION95.71
3.83-18.260.18821360.14422576X-RAY DIFFRACTION93.2

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