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- PDB-8qx5: Helical Carotenoid Protein 4 (HCP4) from Anabaena with bound Cant... -

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Basic information

Entry
Database: PDB / ID: 8qx5
TitleHelical Carotenoid Protein 4 (HCP4) from Anabaena with bound Canthaxanthin
ComponentsOrange carotenoid-binding domain-containing protein
KeywordsPHOTOSYNTHESIS / Photoprotection / soluble proteins / Orange carotenoid protein / Cyanobacteria
Function / homology
Function and homology information


light absorption / phycobilisome / chloride ion binding / plasma membrane-derived thylakoid membrane
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.
Similarity search - Domain/homology
beta,beta-carotene-4,4'-dione / Orange carotenoid-binding domain-containing protein
Similarity search - Component
Biological speciesCyanobacteriota (cyanobacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsSklyar, J. / Wilson, A. / Kirilovsky, D. / Adir, N.
Funding support Israel, 1items
OrganizationGrant numberCountry
Israel Science Foundation1596/21 Israel
CitationJournal: Int.J.Biol.Macromol. / Year: 2024
Title: Insights into energy quenching mechanisms and carotenoid uptake by orange carotenoid protein homologs: HCP4 and CTDH.
Authors: Sklyar, J. / Wilson, A. / Kirilovsky, D. / Adir, N.
History
DepositionOct 22, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 3, 2024Provider: repository / Type: Initial release
Revision 1.1Apr 10, 2024Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)40,0184
Polymers38,8882
Non-polymers1,1302
Water3,351186
1
A: Orange carotenoid-binding domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,0092
Polymers19,4441
Non-polymers5651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Orange carotenoid-binding domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,0092
Polymers19,4441
Non-polymers5651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)59.468, 59.468, 183.780
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number91
Space group name H-MP4122
Space group name HallP4w2c
Symmetry operation#1: x,y,z
#2: -y,x,z+1/4
#3: y,-x,z+3/4
#4: x,-y,-z+1/2
#5: -x,y,-z
#6: -x,-y,z+1/2
#7: y,x,-z+3/4
#8: -y,-x,-z+1/4
Components on special symmetry positions
IDModelComponents
11A-388-

HOH

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Components

#1: Protein Orange carotenoid-binding domain-containing protein


Mass: 19444.033 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cyanobacteriota (cyanobacteria) / Strain: Anabaena / Gene: all4941 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q8YMJ2
#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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 186 / 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: 2.09 Å3/Da / Density % sol: 41.12 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 0.095M sodium citrate tribasic dihydrate pH=5.6, 19% v/v 2-propanol, 19% w/v PEG 4000, 5% glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9537 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Jul 27, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.9→29.73 Å / Num. obs: 27148 / % possible obs: 99.9 % / Redundancy: 26.2 % / CC1/2: 1 / Rmerge(I) obs: 0.089 / Rpim(I) all: 0.024 / Rrim(I) all: 0.092 / Net I/σ(I): 25
Reflection shellResolution: 1.9→1.94 Å / Num. unique obs: 1679 / CC1/2: 0.955

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
pointlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→29.73 Å / SU ML: 0.2205 / Cross valid method: FREE R-VALUE / Phase error: 22.1239
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2175 1357 5.01 %
Rwork0.1936 25713 -
obs-27070 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.9→29.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2398 0 84 186 2668
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00812520
X-RAY DIFFRACTIONf_angle_d0.99533421
X-RAY DIFFRACTIONf_chiral_restr0.058391
X-RAY DIFFRACTIONf_plane_restr0.0093444
X-RAY DIFFRACTIONf_dihedral_angle_d14.4947375
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.9660.36441150.26812505X-RAY DIFFRACTION99.32
1.97-2.040.26911420.22342531X-RAY DIFFRACTION99.93
2.04-2.140.22321350.19632497X-RAY DIFFRACTION100
2.14-2.250.21811380.18362510X-RAY DIFFRACTION99.96
2.25-2.390.20951300.19352553X-RAY DIFFRACTION100
2.39-2.580.25531410.20252537X-RAY DIFFRACTION100
2.58-2.830.191380.18832574X-RAY DIFFRACTION100
2.83-3.240.23611290.18572590X-RAY DIFFRACTION100
3.24-4.090.18671440.16982606X-RAY DIFFRACTION100
4.09-29.730.21371450.20422810X-RAY DIFFRACTION99.8

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