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- PDB-9r84: The C103F Mutant of Apo-C-Terminal Domain Homolog of the Orange C... -

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Basic information

Entry
Database: PDB / ID: 9r84
TitleThe C103F Mutant of Apo-C-Terminal Domain Homolog of the Orange Carotenoid Protein (CTDH) from Anabaena
Components(All4940 protein) x 2
KeywordsPHOTOSYNTHESIS / Cyanobacteria / Carotenoid transport / Orange carotenoid protein homolog
Function / homologyNuclear transport factor 2 (NTF2) domain / Nuclear transport factor 2 domain / NTF2-like domain superfamily / CITRATE ANION / D-MALATE / All4940 protein
Function and homology information
Biological speciesCyanobacteriota (cyanobacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsSklyar, J. / Adir, N.
Funding support Israel, 1items
OrganizationGrant numberCountry
Israel Science Foundation1596/21 Israel
Citation
Journal: Thesis / Year: 2025
Title: Structural Characterization of Carotenoid Binding Proteins in Cyanobacteria and Elucidation of Their Role in Carotenoid Uptake and Transfer Mechanism for Photoprotection
Authors: Sklyar, J.
#1: Journal: To Be Published
Title: Structural Characterization of Carotenoid Binding Proteins in Cyanobacteria and Elucidation of Their Role in Carotenoid Uptake and Transfer Mechanism for Photoprotection PhD thesis (2025)
Authors: Sklyar, J. / Adir, N.
History
DepositionMay 15, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 6, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: All4940 protein
B: All4940 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,1995
Polymers27,7422
Non-polymers4573
Water2,000111
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2630 Å2
ΔGint-11 kcal/mol
Surface area13080 Å2
Unit cell
Length a, b, c (Å)106.532, 63.914, 48.565
Angle α, β, γ (deg.)90.00, 99.46, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-303-

HOH

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Components

#1: Protein All4940 protein


Mass: 13806.472 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cyanobacteriota (cyanobacteria) / Gene: all4940 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q8YMJ3
#2: Protein All4940 protein


Mass: 13935.585 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cyanobacteriota (cyanobacteria) / Gene: all4940 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q8YMJ3
#3: Chemical ChemComp-MLT / D-MALATE / (2R)-2-HYDROXYBUTANEDIOIC ACID / 2-HYDROXY-SUCCINIC ACID


Mass: 134.087 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H6O5
#4: Chemical ChemComp-FLC / CITRATE ANION


Mass: 189.100 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H5O7
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 111 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

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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: 3.01 Å3/Da / Density % sol: 59.18 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 37% Tacsimate

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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 PILATUS3 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: 1.75→37.64 Å / Num. obs: 31011 / % possible obs: 95.1 % / Redundancy: 2.5 % / CC1/2: 0.998 / Net I/σ(I): 20.8
Reflection shellResolution: 1.75→1.78 Å / Num. unique obs: 1684 / CC1/2: 0.933

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.75→37.64 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.63 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2595 2668 4.97 %
Rwork0.2346 --
obs0.2359 30825 84.26 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.75→37.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1911 0 31 111 2053
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081980
X-RAY DIFFRACTIONf_angle_d1.0662699
X-RAY DIFFRACTIONf_dihedral_angle_d8.879267
X-RAY DIFFRACTIONf_chiral_restr0.066307
X-RAY DIFFRACTIONf_plane_restr0.008355
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.75-1.780.33061450.30672860X-RAY DIFFRACTION88
1.78-1.820.33731570.29262845X-RAY DIFFRACTION91
1.82-1.850.3081610.29892848X-RAY DIFFRACTION90
1.85-1.890.33161360.29042803X-RAY DIFFRACTION87
1.89-1.940.30881270.28172586X-RAY DIFFRACTION79
1.94-1.990.33631540.29192566X-RAY DIFFRACTION83
1.99-2.040.28631542733X-RAY DIFFRACTION85
2.04-2.10.32671270.29482566X-RAY DIFFRACTION81
2.1-2.170.29321320.28062700X-RAY DIFFRACTION85
2.17-2.240.31371260.25642717X-RAY DIFFRACTION85
2.24-2.330.28971200.28452674X-RAY DIFFRACTION83
2.33-2.440.2951350.26062739X-RAY DIFFRACTION85
2.44-2.570.27421380.25272667X-RAY DIFFRACTION84
2.57-2.730.31341330.26322672X-RAY DIFFRACTION84
2.73-2.940.28461580.26122653X-RAY DIFFRACTION84
2.94-3.240.27081570.24392653X-RAY DIFFRACTION83
3.24-3.70.24921420.22432550X-RAY DIFFRACTION81
3.71-4.670.19981440.17232612X-RAY DIFFRACTION82
4.67-37.640.1991220.17932619X-RAY DIFFRACTION82

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