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- PDB-6y3d: X-ray structure of thermophilic C-phycocyanin from Galdiera phlegrea -

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Basic information

Entry
Database: PDB / ID: 6y3d
TitleX-ray structure of thermophilic C-phycocyanin from Galdiera phlegrea
Components(C-phycocyanin ...) x 2
KeywordsFLUORESCENT PROTEIN / red algae / C-phycocyanin / pigment / fluorescent / Phycobilisomes
Function / homology
Function and homology information


phycobilisome / chloroplast 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
ACETATE ION / PHYCOCYANOBILIN / C-phycocyanin beta chain / C-phycocyanin alpha subunit
Similarity search - Component
Biological speciesCyanidium caldarium (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsFerraro, G. / Lucignano, R. / Marseglia, A. / Merlino, A.
CitationJournal: Biochim Biophys Acta Bioenerg / Year: 2020
Title: X-ray structure of C-phycocyanin from Galdieria phlegrea: Determinants of thermostability and comparison with a C-phycocyanin in the entire phycobilisome.
Authors: Ferraro, G. / Imbimbo, P. / Marseglia, A. / Lucignano, R. / Monti, D.M. / Merlino, A.
History
DepositionFeb 18, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 30, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
AAA: C-phycocyanin alpha chain
BBB: C-phycocyanin beta chain
CCC: C-phycocyanin alpha chain
DDD: C-phycocyanin beta chain
EEE: C-phycocyanin alpha chain
FFF: C-phycocyanin beta chain
GGG: C-phycocyanin alpha chain
HHH: C-phycocyanin beta chain
III: C-phycocyanin alpha chain
JJJ: C-phycocyanin beta chain
KKK: C-phycocyanin alpha chain
LLL: C-phycocyanin beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)223,59133
Polymers212,78412
Non-polymers10,80721
Water21,8881215
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area60350 Å2
ΔGint-516 kcal/mol
Surface area67910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.030, 189.130, 208.130
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121
Components on special symmetry positions
IDModelComponents
11GGG-340-

HOH

21III-308-

HOH

31KKK-313-

HOH

41KKK-382-

HOH

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Components

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

#1: Protein
C-phycocyanin alpha chain


Mass: 17260.398 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Cyanidium caldarium (eukaryote) / References: UniProt: O19910
#2: Protein
C-phycocyanin beta chain


Mass: 18203.604 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Cyanidium caldarium (eukaryote) / References: UniProt: O19909

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Non-polymers , 4 types, 1236 molecules

#3: Chemical
ChemComp-CYC / PHYCOCYANOBILIN


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


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1215 / 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: 2.78 Å3/Da / Density % sol: 55.7 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.10 M Hepes, 0.20 M magnesium chloride and 9.0 % (w/v) PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 11.2C / Wavelength: 0.96 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jun 2, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96 Å / Relative weight: 1
ReflectionResolution: 1.8→94.744 Å / Num. obs: 217082 / % possible obs: 92.5 % / Redundancy: 4.4 % / CC1/2: 0.981 / Rmerge(I) obs: 0.199 / Rpim(I) all: 0.119 / Rrim(I) all: 0.255 / Net I/σ(I): 2.7
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 3.6 % / Rmerge(I) obs: 1.8 / Num. unique obs: 30323 / CC1/2: 0.061 / % possible all: 79.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
MOSFLMdata reduction
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3brp

3brp


Resolution: 1.8→94.744 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.938 / SU B: 7.529 / SU ML: 0.193 / Cross valid method: FREE R-VALUE / ESU R: 0.143 / ESU R Free: 0.142
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2682 11108 5.123 %
Rwork0.2211 --
all0.223 --
obs-216823 98.661 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 30.779 Å2
Baniso -1Baniso -2Baniso -3
1-1.698 Å2-0 Å20 Å2
2---1.668 Å2-0 Å2
3----0.03 Å2
Refinement stepCycle: LAST / Resolution: 1.8→94.744 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14874 0 788 1215 16877
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.01316018
X-RAY DIFFRACTIONr_bond_other_d0.0010.01714788
X-RAY DIFFRACTIONr_angle_refined_deg1.5981.64521796
X-RAY DIFFRACTIONr_angle_other_deg1.4131.57934098
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.65952020
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.06620.383836
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.401152465
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.18115108
X-RAY DIFFRACTIONr_chiral_restr0.080.22157
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0218782
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023304
X-RAY DIFFRACTIONr_nbd_refined0.230.23849
X-RAY DIFFRACTIONr_symmetry_nbd_other0.190.213736
X-RAY DIFFRACTIONr_nbtor_refined0.1610.27899
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0820.26965
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1980.21074
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0280.24
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1930.211
X-RAY DIFFRACTIONr_nbd_other0.1670.260
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1640.230
X-RAY DIFFRACTIONr_mcbond_it2.3843.0918076
X-RAY DIFFRACTIONr_mcbond_other2.383.098074
X-RAY DIFFRACTIONr_mcangle_it3.3024.62510096
X-RAY DIFFRACTIONr_mcangle_other3.3034.62610097
X-RAY DIFFRACTIONr_scbond_it3.43.4387942
X-RAY DIFFRACTIONr_scbond_other3.43.4387943
X-RAY DIFFRACTIONr_scangle_it5.1315.00811700
X-RAY DIFFRACTIONr_scangle_other5.1315.00811701
X-RAY DIFFRACTIONr_lrange_it6.24438.2918643
X-RAY DIFFRACTIONr_lrange_other6.16937.98718349
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.8470.4718350.4714490X-RAY DIFFRACTION95.4829
1.847-1.8970.4197320.41914248X-RAY DIFFRACTION95.2926
1.897-1.9520.4047740.39713967X-RAY DIFFRACTION96.561
1.952-2.0120.3937580.38413732X-RAY DIFFRACTION97.6415
2.012-2.0780.3847490.37313421X-RAY DIFFRACTION98.3959
2.078-2.1510.3767130.34813112X-RAY DIFFRACTION99.3389
2.151-2.2330.3646760.31212713X-RAY DIFFRACTION99.4873
2.233-2.3240.3226960.26712208X-RAY DIFFRACTION99.7912
2.324-2.4270.3075840.23511828X-RAY DIFFRACTION99.6228
2.427-2.5450.2875930.2111282X-RAY DIFFRACTION99.8486
2.545-2.6830.2775670.19810762X-RAY DIFFRACTION99.9206
2.683-2.8460.2655680.18310201X-RAY DIFFRACTION99.9165
2.846-3.0420.2395290.1789550X-RAY DIFFRACTION99.8514
3.042-3.2860.2454970.1798955X-RAY DIFFRACTION99.9154
3.286-3.5990.2184230.1738259X-RAY DIFFRACTION99.5186
3.599-4.0240.2024260.1557504X-RAY DIFFRACTION99.7735
4.024-4.6450.1773360.1416682X-RAY DIFFRACTION99.9288
4.645-5.6880.2223060.1635678X-RAY DIFFRACTION99.9833
5.688-8.0370.2182170.1624500X-RAY DIFFRACTION99.8941
8-100.1531290.1492623X-RAY DIFFRACTION99.7463

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