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- PDB-8z20: Crystal structure analysis of thermotolerant Oscillatoria Phycocyanin -

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Basic information

Entry
Database: PDB / ID: 8z20
TitleCrystal structure analysis of thermotolerant Oscillatoria Phycocyanin
Components
  • Phycocyanin subunit alpha
  • Phycocyanin subunit beta
KeywordsPHOTOSYNTHESIS / Phycocyanin / Oscillatoria / thermotolerant / phycobiliproteins
Function / homology
Function and homology information


phycobilisome / plasma membrane-derived thylakoid membrane / photosynthesis
Similarity search - Function
Phycocyanin, alpha subunit / Phycocyanin, beta subunit / Phycobilisome, alpha/beta subunit / Phycobilisome, alpha/beta subunit superfamily / Phycobilisome protein / Globin-like superfamily
Similarity search - Domain/homology
PHYCOCYANOBILIN / Phycocyanin subunit alpha / Phycocyanin subunit beta
Similarity search - Component
Biological speciesOscillatoria sp. N9DM (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsPatel, S.N. / Sonani, R.R. / Gupta, G.D. / Upadhyaya, C.T. / Sonavane, B.P. / Singh, N.K. / Kumar, V. / Madamwar, D.
Funding support India, 1items
OrganizationGrant numberCountry
Department of Science & Technology (DST, India)GUJCOST/STI/2021-22/3878 India
CitationJournal: Febs Lett. / Year: 2025
Title: Structure and stability of phycocyanin from thermotolerant Oscillatoria.
Authors: Patel, S.N. / Sonani, R.R. / Gupta, G.D. / Singh, N.K. / Upadhyaya, C. / Sonavane, B. / Amin, S. / Kumar, V. / Madamwar, D.
History
DepositionApr 12, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 16, 2025Provider: repository / Type: Initial release
Revision 1.1Jun 11, 2025Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
F: Phycocyanin subunit beta
K: Phycocyanin subunit alpha
H: Phycocyanin subunit beta
B: Phycocyanin subunit beta
D: Phycocyanin subunit beta
J: Phycocyanin subunit beta
L: Phycocyanin subunit beta
A: Phycocyanin subunit alpha
C: Phycocyanin subunit alpha
E: Phycocyanin subunit alpha
G: Phycocyanin subunit alpha
I: Phycocyanin subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)225,62432
Polymers214,84312
Non-polymers10,78120
Water5,873326
1
F: Phycocyanin subunit beta
K: Phycocyanin subunit alpha
B: Phycocyanin subunit beta
L: Phycocyanin subunit beta
A: Phycocyanin subunit alpha
E: Phycocyanin subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,90417
Polymers107,4226
Non-polymers5,48211
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area24390 Å2
ΔGint-239 kcal/mol
Surface area39890 Å2
MethodPISA
2
H: Phycocyanin subunit beta
D: Phycocyanin subunit beta
J: Phycocyanin subunit beta
C: Phycocyanin subunit alpha
G: Phycocyanin subunit alpha
I: Phycocyanin subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,72015
Polymers107,4226
Non-polymers5,2989
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area24260 Å2
ΔGint-243 kcal/mol
Surface area39610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.012, 153.728, 207.034
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Phycocyanin subunit beta


Mass: 18233.592 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Details: light harvesting fluorescent phycobiliprotein / Source: (natural) Oscillatoria sp. N9DM (bacteria) / References: UniProt: A0A930TN56
#2: Protein
Phycocyanin subunit alpha


Mass: 17573.596 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Details: light harvesting fluorescent phycobiliprotein / Source: (natural) Oscillatoria sp. N9DM (bacteria) / References: UniProt: A0A930TJP2
#3: Chemical
ChemComp-CYC / PHYCOCYANOBILIN


Mass: 588.694 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: C33H40N4O6 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 326 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.97 Å3/Da / Density % sol: 58.58 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 0.2M posttasium formate, 20% (W/V) PEG 3350 at pH 7.3

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: RRCAT INDUS-2 / Beamline: PX-BL21 / Wavelength: 0.979 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Nov 17, 2020
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.5→40.01 Å / Num. obs: 93421 / % possible obs: 99.9 % / Redundancy: 6.3 % / CC1/2: 0.997 / Net I/σ(I): 10.3
Reflection shellResolution: 2.5→2.54 Å / Num. unique obs: 4580 / CC1/2: 0.701

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Processing

Software
NameVersionClassification
REFMAC5.8.0415refinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→40.01 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.904 / SU B: 10.373 / SU ML: 0.223 / Cross valid method: THROUGHOUT / ESU R: 0.408 / ESU R Free: 0.281 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25964 4630 5 %RANDOM
Rwork0.19668 ---
obs0.19976 88716 99.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 41.505 Å2
Baniso -1Baniso -2Baniso -3
1-0.51 Å20 Å2-0 Å2
2--0.91 Å20 Å2
3----1.43 Å2
Refinement stepCycle: 1 / Resolution: 2.5→40.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15772 0 12 326 16110
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.01216058
X-RAY DIFFRACTIONr_bond_other_d0.0010.01615052
X-RAY DIFFRACTIONr_angle_refined_deg1.6541.65921854
X-RAY DIFFRACTIONr_angle_other_deg0.5481.57234373
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.69551992
X-RAY DIFFRACTIONr_dihedral_angle_2_deg6.4955222
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.43102464
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0720.22390
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0219872
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023696
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.9664.1178004
X-RAY DIFFRACTIONr_mcbond_other3.9664.1178004
X-RAY DIFFRACTIONr_mcangle_it5.857.3899984
X-RAY DIFFRACTIONr_mcangle_other5.857.3899985
X-RAY DIFFRACTIONr_scbond_it4.5924.3848054
X-RAY DIFFRACTIONr_scbond_other4.5924.3848053
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.9647.88611871
X-RAY DIFFRACTIONr_long_range_B_refined8.8438.7718640
X-RAY DIFFRACTIONr_long_range_B_other8.8438.7718641
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.334 330 -
Rwork0.276 6474 -
obs--99.96 %

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