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- PDB-6yyj: Crystal structure of native Phycocyanin from T. elongatus in spac... -

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Basic information

Entry
Database: PDB / ID: 6yyj
TitleCrystal structure of native Phycocyanin from T. elongatus in spacegroup P21212 at 2.1 Angstroms
Components(C-phycocyanin ...) x 2
KeywordsPHOTOSYNTHESIS / Phytocyanin / Antenna Protein / Chromophore / Light-harvesting
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
TRIETHYLENE GLYCOL / Chem-PXQ / C-phycocyanin alpha subunit / C-phycocyanin beta subunit
Similarity search - Component
Biological speciesThermosynechococcus elongatus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.16 Å
AuthorsFeiler, C.G. / Falke, S. / Sarrou, I.
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2021
Title: C-phycocyanin as a highly attractive model system in protein crystallography: unique crystallization properties and packing-diversity screening.
Authors: Sarrou, I. / Feiler, C.G. / Falke, S. / Peard, N. / Yefanov, O. / Chapman, H.
History
DepositionMay 5, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 20, 2021Provider: repository / Type: Initial release
Revision 1.1Feb 17, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _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
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)113,86824
Polymers107,0206
Non-polymers6,84818
Water2,954164
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16970 Å2
ΔGint-57 kcal/mol
Surface area40210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)118.363, 98.231, 104.600
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Space group name HallP22ab
Components on special symmetry positions
IDModelComponents
11A-324-

HOH

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Components

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C-phycocyanin ... , 2 types, 6 molecules ACEBDF

#1: Protein C-phycocyanin alpha chain


Mass: 17456.631 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Thermosynechococcus elongatus (bacteria) / References: UniProt: P50032
#2: Protein C-phycocyanin beta chain


Mass: 18216.652 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Thermosynechococcus elongatus (bacteria) / References: UniProt: P50033

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Non-polymers , 4 types, 182 molecules

#3: Chemical
ChemComp-PXQ / 3-[5-[[(3~{R},4~{R})-3-ethyl-4-methyl-5-oxidanylidene-3,4-dihydropyrrol-2-yl]methyl]-2-[[5-[(~{Z})-(4-ethyl-3-methyl-5-oxidanylidene-pyrrol-2-ylidene)methyl]-3-(3-hydroxy-3-oxopropyl)-4-methyl-1~{H}-pyrrol-2-yl]methyl]-4-methyl-1~{H}-pyrrol-3-yl]propanoic acid


Mass: 590.710 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C33H42N4O6
#4: Chemical
ChemComp-PGE / TRIETHYLENE GLYCOL / Polyethylene glycol


Mass: 150.173 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C6H14O4
#5: Chemical
ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID / MES (buffer)


Mass: 195.237 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 164 / 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: 2.84 Å3/Da / Density % sol: 56.71 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 1,2% Cholic Acid derivatives mix, 0.1M Buffer System1, 50% precipitant Mix1

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 1.0332 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Dec 3, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.16→47.84 Å / Num. obs: 66066 / % possible obs: 99.84 % / Redundancy: 7.4 % / Biso Wilson estimate: 38.63 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.23 / Rpim(I) all: 0.098 / Rrim(I) all: 0.268 / Χ2: 1.01 / Net I/σ(I): 7
Reflection shellResolution: 2.16→2.21 Å / Rmerge(I) obs: 2.873 / Mean I/σ(I) obs: 0.7 / Num. unique obs: 6450 / CC1/2: 0.263 / Rpim(I) all: 1.217 / Rrim(I) all: 3.338 / Χ2: 1.01 / % possible all: 99

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6YPQ

6ypq


Resolution: 2.16→47.84 Å / SU ML: 0.3462 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.4441
RfactorNum. reflection% reflection
Rfree0.2582 2100 3.18 %
Rwork0.2042 --
obs0.206 65988 99.48 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 44.98 Å2
Refinement stepCycle: LAST / Resolution: 2.16→47.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7485 0 485 165 8135
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01268126
X-RAY DIFFRACTIONf_angle_d1.541411048
X-RAY DIFFRACTIONf_chiral_restr0.05041209
X-RAY DIFFRACTIONf_plane_restr0.00691420
X-RAY DIFFRACTIONf_dihedral_angle_d20.62681405
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.16-2.210.38851300.33763943X-RAY DIFFRACTION92.93
2.21-2.260.39541390.31674211X-RAY DIFFRACTION99.89
2.26-2.320.37631390.29234235X-RAY DIFFRACTION99.89
2.32-2.390.31271390.27064235X-RAY DIFFRACTION99.95
2.39-2.470.30471390.25174223X-RAY DIFFRACTION99.98
2.47-2.560.29251390.244248X-RAY DIFFRACTION99.95
2.56-2.660.34911390.244230X-RAY DIFFRACTION99.98
2.66-2.780.30851390.22734233X-RAY DIFFRACTION99.98
2.78-2.930.29491410.22024276X-RAY DIFFRACTION99.98
2.93-3.110.27771390.21984253X-RAY DIFFRACTION99.98
3.11-3.350.26091410.21584280X-RAY DIFFRACTION99.93
3.35-3.690.24211410.18254300X-RAY DIFFRACTION100
3.69-4.220.21841420.15934323X-RAY DIFFRACTION99.98
4.22-5.320.18721430.16224366X-RAY DIFFRACTION99.93
5.32-47.840.23321500.18344532X-RAY DIFFRACTION99.85

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