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- PDB-9h41: Apo-Helical Carotenoid Protein 4 (HCP4) from Anabaena G152C mutant -

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Basic information

Entry
Database: PDB / ID: 9h41
TitleApo-Helical Carotenoid Protein 4 (HCP4) from Anabaena G152C mutant
ComponentsOrange carotenoid-binding domain-containing protein
KeywordsPHOTOSYNTHESIS / Non photochemical quenching Orange carotenoid binding protein Cyanobacteria Phycobilisome Photoprotection
Function / homologylight absorption / 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. / phycobilisome / chloride ion binding / plasma membrane-derived thylakoid membrane / Orange carotenoid-binding domain-containing protein
Function and homology information
Biological speciesNostoc sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.09 Å
AuthorsSklyar, J. / Adir, N.
Funding support Israel, 1items
OrganizationGrant numberCountry
Israel Science Foundation1596/21 Israel
CitationJournal: Int.J.Biol.Macromol. / Year: 2025
Title: The apo-HCP4 structure reveals facets of carotenoid uptake.
Authors: Sklyar, J. / Glaser, F. / Adir, N.
History
DepositionOct 17, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 11, 2025Provider: 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 domain-containing protein


Theoretical massNumber of molelcules
Total (without water)18,4731
Polymers18,4731
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area8140 Å2
2
A: Orange carotenoid-binding domain-containing protein

A: Orange carotenoid-binding domain-containing protein


Theoretical massNumber of molelcules
Total (without water)36,9462
Polymers36,9462
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-y,-x,-z+1/21
Buried area840 Å2
ΔGint-12 kcal/mol
Surface area15440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.871, 60.871, 112.389
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

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


Mass: 18472.998 Da / Num. of mol.: 1 / Mutation: G151C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nostoc sp. (strain PCC 7120 / SAG 25.82 / UTEX 2576) (bacteria)
Gene: all4941 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q8YMJ2
Has protein modificationY

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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: 2.7 Å3/Da / Density % sol: 56.35 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.08M Tris pH 8.5, 1.6M Ammonium dihydrogen phosphate, 20% v/v Glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.9655 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 15, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9655 Å / Relative weight: 1
ReflectionResolution: 3.09→9.97 Å / Num. obs: 40807 / % possible obs: 96.1 % / Redundancy: 10.1 % / CC1/2: 0.994 / Rmerge(I) obs: 0.14 / Net I/σ(I): 11.9
Reflection shellResolution: 3.09→3.34 Å / Num. unique obs: 4175 / CC1/2: 0.943

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
XDSdata reduction
pointlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.09→9.97 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.62 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2425 347 4.95 %
Rwork0.2018 --
obs0.2039 7010 98.12 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.09→9.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1160 0 0 0 1160
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01
X-RAY DIFFRACTIONf_angle_d1.161
X-RAY DIFFRACTIONf_dihedral_angle_d6.163158
X-RAY DIFFRACTIONf_chiral_restr0.074188
X-RAY DIFFRACTIONf_plane_restr0.007203
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.09-3.860.26241790.23083257X-RAY DIFFRACTION96
3.86-9.970.22921680.18373406X-RAY DIFFRACTION100

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