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- PDB-8xf1: Crystal structure of the dissociated C-phycocyanin beta-chain fro... -

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Basic information

Entry
Database: PDB / ID: 8xf1
TitleCrystal structure of the dissociated C-phycocyanin beta-chain from Thermoleptolyngbya sp. O-77
ComponentsC-phycocyanin beta chain
KeywordsPHOTOSYNTHESIS / dissociated subunit / C-phycocyanin
Function / homologyPHYCOCYANOBILIN
Function and homology information
Biological speciesLeptolyngbya sp. O-77 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.94 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

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Assembly

Deposited unit
A: C-phycocyanin beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,2753
Polymers18,0971
Non-polymers1,1772
Water1,74797
1
A: C-phycocyanin beta chain
hetero molecules

A: C-phycocyanin beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,5506
Polymers36,1952
Non-polymers2,3554
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_566x,-y+1,-z+11
Buried area7500 Å2
ΔGint-87 kcal/mol
Surface area16300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.491, 145.059, 66.129
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein C-phycocyanin beta chain


Mass: 18097.465 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leptolyngbya sp. O-77 (bacteria)
#2: Chemical ChemComp-CYC / PHYCOCYANOBILIN


Mass: 588.694 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C33H40N4O6
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 97 / 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: 2.57 Å3/Da / Density % sol: 52.12 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 20% (w/v) PEG3350, 0.2 M Mg(CH3COO)2 4H2O

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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: Apr 5, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.94→50 Å / Num. obs: 26569 / % possible obs: 99.9 % / Redundancy: 6.9 % / CC1/2: 0.998 / Net I/σ(I): 10
Reflection shellResolution: 1.94→2.05 Å / Num. unique obs: 4294 / CC1/2: 0.55

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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: 1.94→48.87 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.08 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2364 2672 10.07 %
Rwork0.194 --
obs0.1984 26538 99.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.94→48.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1256 0 86 97 1439
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081383
X-RAY DIFFRACTIONf_angle_d1.5471885
X-RAY DIFFRACTIONf_dihedral_angle_d11.965223
X-RAY DIFFRACTIONf_chiral_restr0.051211
X-RAY DIFFRACTIONf_plane_restr0.01245
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.94-1.970.46071370.37511253X-RAY DIFFRACTION98
1.97-2.010.38291400.34991248X-RAY DIFFRACTION100
2.01-2.050.37941430.32831244X-RAY DIFFRACTION99
2.05-2.10.36471370.30881235X-RAY DIFFRACTION100
2.1-2.150.43511400.30081294X-RAY DIFFRACTION100
2.15-2.20.26651350.2741232X-RAY DIFFRACTION100
2.2-2.260.3041460.2521277X-RAY DIFFRACTION100
2.26-2.330.26791400.22281253X-RAY DIFFRACTION100
2.33-2.40.24721430.22591244X-RAY DIFFRACTION100
2.4-2.490.24841420.211257X-RAY DIFFRACTION100
2.49-2.590.29241460.2161258X-RAY DIFFRACTION100
2.59-2.70.24231370.20661260X-RAY DIFFRACTION100
2.7-2.840.25631420.19261247X-RAY DIFFRACTION100
2.85-3.020.25951440.19411258X-RAY DIFFRACTION100
3.02-3.260.20681390.18081261X-RAY DIFFRACTION100
3.26-3.580.22161440.16841251X-RAY DIFFRACTION100
3.59-4.10.20411410.15051250X-RAY DIFFRACTION100
4.1-5.170.19111360.14641270X-RAY DIFFRACTION100
5.17-48.870.17891400.1731274X-RAY DIFFRACTION100

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