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- PDB-8pyh: Crystal structure of the Orange Carotenoid Protein 2 (OCP2) from ... -

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Basic information

Entry
Database: PDB / ID: 8pyh
TitleCrystal structure of the Orange Carotenoid Protein 2 (OCP2) from Crinalium epipsammum PCC 9333
ComponentsOrange carotenoid-binding protein
KeywordsPHOTOSYNTHESIS / Orange Carotenoid Protein / OCP / OCP2
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 / beta,beta-caroten-4-one / Orange carotenoid-binding protein
Similarity search - Component
Biological speciesCrinalium epipsammum PCC 9333 (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsBoyko, K.M. / Varfolomeeva, L.A. / Slonimskiy, Y.B. / Maksimov, E.G. / Popov, V.O. / Sluchanko, N.N.
Funding support Russian Federation, 2items
OrganizationGrant numberCountry
Ministry of Science and Higher Education of the Russian Federation075-15-2021-1354 Russian Federation
Russian Science Foundation21-44-00005 Russian Federation
CitationJournal: Int.J.Biol.Macromol. / Year: 2024
Title: Structural framework for the understanding spectroscopic and functional signatures of the cyanobacterial Orange Carotenoid Protein families.
Authors: Sluchanko, N.N. / Maksimov, E.G. / Slonimskiy, Y.B. / Varfolomeeva, L.A. / Bukhanko, A.Y. / Egorkin, N.A. / Tsoraev, G.V. / Khrenova, M.G. / Ge, B. / Qin, S. / Boyko, K.M. / Popov, V.O.
History
DepositionJul 25, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 3, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)71,3895
Polymers70,2282
Non-polymers1,1613
Water5,459303
1
A: Orange carotenoid-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,7243
Polymers35,1141
Non-polymers6102
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Orange carotenoid-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,6652
Polymers35,1141
Non-polymers5511
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)60.054, 103.727, 109.620
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Orange carotenoid-binding protein


Mass: 35113.914 Da / Num. of mol.: 2 / Mutation: E26A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Crinalium epipsammum PCC 9333 (bacteria)
Gene: Cri9333_0045 / Production host: Escherichia coli (E. coli) / References: UniProt: K9VSN3
#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: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 303 / 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: 2.45 Å3/Da / Density % sol: 49.78 %
Crystal growTemperature: 288 K / Method: vapor diffusion, sitting drop
Details: 0.1 M Imidazole pH 6.5, 1.0 M Sodium acetate trihydrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54184 Å
DetectorType: RIGAKU HyPix-6000HE / Detector: PIXEL / Date: Apr 14, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54184 Å / Relative weight: 1
ReflectionResolution: 2.2→22.2 Å / Num. obs: 35514 / % possible obs: 99.7 % / Redundancy: 7.5 % / CC1/2: 0.993 / Rmerge(I) obs: 0.13 / Rpim(I) all: 0.051 / Rrim(I) all: 0.14 / Χ2: 0.96 / Net I/σ(I): 12.3 / Num. measured all: 265057
Reflection shellResolution: 2.2→2.27 Å / % possible obs: 98.2 % / Redundancy: 7.8 % / Rmerge(I) obs: 0.384 / Num. measured all: 23129 / Num. unique obs: 2978 / CC1/2: 0.874 / Rpim(I) all: 0.146 / Rrim(I) all: 0.412 / Χ2: 0.96 / Net I/σ(I) obs: 5.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0419refinement
Aimlessdata scaling
CrysalisProdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→22.2 Å / Cor.coef. Fo:Fc: 0.918 / Cor.coef. Fo:Fc free: 0.873 / SU B: 5.842 / SU ML: 0.151 / Cross valid method: THROUGHOUT / ESU R: 0.055 / ESU R Free: 0.043 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22693 1821 5.1 %RANDOM
Rwork0.17739 ---
obs0.17991 33599 85.45 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.65 Å2
Baniso -1Baniso -2Baniso -3
1--7.07 Å2-0 Å2-0 Å2
2--14.17 Å20 Å2
3----7.1 Å2
Refinement stepCycle: 1 / Resolution: 2.2→22.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4824 0 86 303 5213
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0125099
X-RAY DIFFRACTIONr_bond_other_d0.0040.0164825
X-RAY DIFFRACTIONr_angle_refined_deg2.0481.6456962
X-RAY DIFFRACTIONr_angle_other_deg0.81.56411113
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.1995655
X-RAY DIFFRACTIONr_dihedral_angle_2_deg15.798559
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.38110821
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1010.2779
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.026127
X-RAY DIFFRACTIONr_gen_planes_other0.0040.021133
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.5841.9722563
X-RAY DIFFRACTIONr_mcbond_other2.5791.9712562
X-RAY DIFFRACTIONr_mcangle_it3.9083.543204
X-RAY DIFFRACTIONr_mcangle_other3.9083.5413205
X-RAY DIFFRACTIONr_scbond_it2.5912.0232536
X-RAY DIFFRACTIONr_scbond_other2.5912.0232537
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.9193.6783746
X-RAY DIFFRACTIONr_long_range_B_refined6.321.585881
X-RAY DIFFRACTIONr_long_range_B_other6.321.575882
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.2→2.21 Å
RfactorNum. reflection% reflection
Rfree0 0 -
Rwork0 0 -
obs--0 %

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