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- PDB-8xf2: Crystal structure of the reassembled C-phycocyanin hexamer from T... -

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Basic information

Entry
Database: PDB / ID: 8xf2
TitleCrystal structure of the reassembled C-phycocyanin hexamer from Thermoleptolyngbya sp. O-77
Components(C-phycocyanin ...) x 2
KeywordsPHOTOSYNTHESIS / Hexamer
Function / homologyPHYCOCYANOBILIN / PHOSPHATE ION
Function and homology information
Biological speciesLeptolyngbya sp. O-77 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.98 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
E: C-phycocyanin alpha chain
F: C-phycocyanin beta chain
G: C-phycocyanin alpha chain
H: C-phycocyanin beta chain
I: C-phycocyanin alpha chain
J: C-phycocyanin beta chain
K: C-phycocyanin alpha chain
L: C-phycocyanin beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)224,89836
Polymers213,94812
Non-polymers10,95024
Water36,5342028
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area61210 Å2
ΔGint-547 kcal/mol
Surface area68280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)107.729, 115.069, 186.989
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121
Components on special symmetry positions
IDModelComponents
11L-379-

HOH

21L-430-

HOH

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Components

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C-phycocyanin ... , 2 types, 12 molecules ACEGIKBDFHJL

#1: Protein
C-phycocyanin alpha chain


Mass: 17560.531 Da / Num. of mol.: 6 / 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.: 6 / Source method: isolated from a natural source / Source: (natural) Leptolyngbya sp. O-77 (bacteria)

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Non-polymers , 4 types, 2052 molecules

#3: Chemical
ChemComp-CYC / PHYCOCYANOBILIN


Mass: 588.694 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: C33H40N4O6
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2028 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.71 Å3/Da / Density % sol: 54.59 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 8% Tacsimate (pH 5.0), 20% polyethylene glycol 3350

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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: 1.98→50 Å / Num. obs: 162251 / % possible obs: 99.9 % / Redundancy: 7 % / CC1/2: 0.991 / Net I/σ(I): 7.1
Reflection shellResolution: 1.98→2.09 Å / Num. unique obs: 25284 / CC1/2: 0.435

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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: 1.98→49 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.91 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2212 1988 1.23 %
Rwork0.1827 --
obs0.1832 162251 99.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.98→49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14997 0 792 2028 17817
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00316289
X-RAY DIFFRACTIONf_angle_d1.22222227
X-RAY DIFFRACTIONf_dihedral_angle_d9.7792556
X-RAY DIFFRACTIONf_chiral_restr0.0342451
X-RAY DIFFRACTIONf_plane_restr0.0042900
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.98-2.030.35071390.304411248X-RAY DIFFRACTION99
2.03-2.080.34831320.266411341X-RAY DIFFRACTION100
2.08-2.140.28761530.231611328X-RAY DIFFRACTION100
2.14-2.210.24731360.219511361X-RAY DIFFRACTION100
2.21-2.290.22761470.208311371X-RAY DIFFRACTION100
2.29-2.380.23171390.202911349X-RAY DIFFRACTION100
2.38-2.490.22581290.203911425X-RAY DIFFRACTION100
2.49-2.620.24281470.189611401X-RAY DIFFRACTION100
2.62-2.790.23791470.190611381X-RAY DIFFRACTION100
2.79-30.2461420.187511464X-RAY DIFFRACTION100
3-3.30.24111400.182311487X-RAY DIFFRACTION100
3.3-3.780.19471410.165311518X-RAY DIFFRACTION100
3.78-4.760.16271480.140611627X-RAY DIFFRACTION100
4.76-490.18611480.152411962X-RAY DIFFRACTION100

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