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- PDB-8xf3: Crystal structure of the reassembled C-phycocyanin octamer from T... -

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Basic information

Entry
Database: PDB / ID: 8xf3
TitleCrystal structure of the reassembled C-phycocyanin octamer from Thermoleptolyngbya sp. O-77
Components
  • C-phycocyanin alpha chain
  • C-phycocyanin beta chain
KeywordsPHOTOSYNTHESIS / Octamer
Function / homologyPHYCOCYANOBILIN / PHOSPHATE ION
Function and homology information
Biological speciesLeptolyngbya sp. O-77 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsNguyen, H.K. / Teramoto, T. / Kakuta, Y. / Yoon, K.S.
Funding support Japan, 2items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)JP26000008 Japan
Japan Society for the Promotion of Science (JSPS)JP15K05566 Japan
CitationJournal: J.Biosci.Bioeng. / Year: 2024
Title: Disassembly and reassembly of the non-conventional thermophilic C-phycocyanin.
Authors: Nguyen, H.K. / Minato, T. / Teramoto, T. / Ogo, S. / Kakuta, Y. / Yoon, K.S.
History
DepositionDec 13, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 22, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: C-phycocyanin alpha chain
B: C-phycocyanin beta chain
C: C-phycocyanin alpha chain
D: C-phycocyanin beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,94311
Polymers71,3164
Non-polymers3,6277
Water37821
1
A: C-phycocyanin alpha chain
B: C-phycocyanin beta chain
C: C-phycocyanin alpha chain
D: C-phycocyanin beta chain
hetero molecules

A: C-phycocyanin alpha chain
B: C-phycocyanin beta chain
C: C-phycocyanin alpha chain
D: C-phycocyanin beta chain
hetero molecules

A: C-phycocyanin alpha chain
B: C-phycocyanin beta chain
C: C-phycocyanin alpha chain
D: C-phycocyanin beta chain
hetero molecules

A: C-phycocyanin alpha chain
B: C-phycocyanin beta chain
C: C-phycocyanin alpha chain
D: C-phycocyanin beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)299,77344
Polymers285,26416
Non-polymers14,50928
Water28816
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation15_555y,-x,z1
crystal symmetry operation16_555-y,x,z1
Buried area77040 Å2
ΔGint-679 kcal/mol
Surface area94590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)230.800, 230.800, 230.800
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number211
Space group name H-MI432

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Components

#1: Protein C-phycocyanin alpha chain


Mass: 17560.531 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Leptolyngbya sp. O-77 (bacteria)
#2: Protein C-phycocyanin beta chain


Mass: 18097.465 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Leptolyngbya sp. O-77 (bacteria)
#3: Chemical
ChemComp-CYC / PHYCOCYANOBILIN


Mass: 588.694 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C33H40N4O6
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 21 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 3.59 Å3/Da / Density % sol: 65.75 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 1.6M sodium chloride, 8% polyethylene glycol 6000, 20% glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL45XU / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 4, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 36274 / % possible obs: 100 % / Redundancy: 63 % / CC1/2: 0.998 / Net I/σ(I): 14.3
Reflection shellResolution: 2.5→2.64 Å / Num. unique obs: 5721 / CC1/2: 0.554

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→47.11 Å / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 26.7 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2396 1995 5.5 %
Rwork0.2017 --
obs0.2038 36274 99.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.5→47.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4997 0 263 21 5281
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0035421
X-RAY DIFFRACTIONf_angle_d1.1457388
X-RAY DIFFRACTIONf_dihedral_angle_d9.963845
X-RAY DIFFRACTIONf_chiral_restr0.033812
X-RAY DIFFRACTIONf_plane_restr0.004963
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.560.4211360.38972322X-RAY DIFFRACTION96
2.56-2.630.34011400.30442409X-RAY DIFFRACTION100
2.63-2.710.34841390.29952395X-RAY DIFFRACTION100
2.71-2.80.30971420.3092427X-RAY DIFFRACTION100
2.8-2.90.36241420.3072438X-RAY DIFFRACTION100
2.9-3.010.29711400.29842414X-RAY DIFFRACTION100
3.01-3.150.31741410.25812424X-RAY DIFFRACTION100
3.15-3.320.29871410.24432440X-RAY DIFFRACTION100
3.32-3.520.28111430.2382439X-RAY DIFFRACTION100
3.52-3.80.2331430.19772469X-RAY DIFFRACTION100
3.8-4.180.20151430.16982449X-RAY DIFFRACTION100
4.18-4.780.17831430.14422479X-RAY DIFFRACTION100
4.78-6.020.21611480.16812518X-RAY DIFFRACTION100
6.03-47.110.17341540.14642656X-RAY DIFFRACTION100

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