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- PDB-6yqg: Crystal structure of native Phycocyanin in spacegroup P63 at 1.45... -

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Basic information

Entry
Database: PDB / ID: 6yqg
TitleCrystal structure of native Phycocyanin in spacegroup P63 at 1.45 Angstroms.
Components
  • C-phycocyanin alpha chain
  • C-phycocyanin beta chain
KeywordsPHOTOSYNTHESIS / C-Phycocyanin / Antenna Protein / Light harvest
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 / Tetracaine / C-phycocyanin alpha subunit / C-phycocyanin beta subunit
Similarity search - Component
Biological speciesThermosynechococcus elongatus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 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
DepositionApr 17, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,7046
Polymers35,6732
Non-polymers2,0304
Water7,224401
1
A: C-phycocyanin alpha chain
B: C-phycocyanin beta chain
hetero molecules

A: C-phycocyanin alpha chain
B: C-phycocyanin beta chain
hetero molecules

A: C-phycocyanin alpha chain
B: C-phycocyanin beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)113,11118
Polymers107,0206
Non-polymers6,09112
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-y-1,x-y,z1
crystal symmetry operation3_445-x+y-1,-x-1,z1
Buried area24480 Å2
ΔGint-242 kcal/mol
Surface area39790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)108.208, 108.208, 66.050
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number173
Space group name H-MP63
Space group name HallP6c
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/2
#3: y,-x+y,z+1/2
#4: -y,x-y,z
#5: -x+y,-x,z
#6: -x,-y,z+1/2

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Components

#1: Protein C-phycocyanin alpha chain


Mass: 17456.631 Da / Num. of mol.: 1 / 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.: 1 / Source method: isolated from a natural source / Details: residue 72: N4-methylasparagine / Source: (natural) Thermosynechococcus elongatus (bacteria) / References: UniProt: P50033
#3: Chemical ChemComp-CYC / PHYCOCYANOBILIN


Mass: 588.694 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C33H40N4O6
#4: Chemical ChemComp-TE4 / Tetracaine / 2-(dimethylamino)ethyl 4-(butylamino)benzoate


Mass: 264.363 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H24N2O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 401 / 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: 3.13 Å3/Da / Density % sol: 60.69 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0,8% Anesthetic alkaloids mix, 0,1M Buffer System2 ,50% Precipitant mix2

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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 PILATUS 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: 1.45→46.86 Å / Num. obs: 153519 / % possible obs: 99.8 % / Redundancy: 5.72 % / Biso Wilson estimate: 23.61 Å2 / CC1/2: 0.999 / Rrim(I) all: 0.096 / Net I/σ(I): 9.95
Reflection shellResolution: 1.45→1.54 Å / Num. unique obs: 24621 / CC1/2: 0.246

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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: 1.45→46.86 Å / SU ML: 0.258 / Cross valid method: FREE R-VALUE / σ(F): 1.07 / Phase error: 27.9037
RfactorNum. reflection% reflection
Rfree0.208 2100 1.37 %
Rwork0.1783 --
obs0.1787 153468 99.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 32.84 Å2
Refinement stepCycle: LAST / Resolution: 1.45→46.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2498 0 148 402 3048
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00832731
X-RAY DIFFRACTIONf_angle_d1.24773726
X-RAY DIFFRACTIONf_chiral_restr0.0617408
X-RAY DIFFRACTIONf_plane_restr0.0057485
X-RAY DIFFRACTIONf_dihedral_angle_d24.4548473
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.45-1.480.48211370.50349886X-RAY DIFFRACTION97.37
1.48-1.520.43141390.438210037X-RAY DIFFRACTION99.68
1.52-1.560.41441440.395910125X-RAY DIFFRACTION99.72
1.56-1.610.35471390.336410071X-RAY DIFFRACTION99.81
1.61-1.660.32641400.306210130X-RAY DIFFRACTION99.74
1.66-1.720.29231400.273310083X-RAY DIFFRACTION99.9
1.72-1.790.26951390.250410090X-RAY DIFFRACTION99.88
1.79-1.870.22331400.224410156X-RAY DIFFRACTION99.98
1.87-1.970.23221400.195610081X-RAY DIFFRACTION99.97
1.97-2.090.22721380.169510119X-RAY DIFFRACTION99.98
2.09-2.250.19811380.154310119X-RAY DIFFRACTION99.99
2.25-2.480.18351400.14810093X-RAY DIFFRACTION99.98
2.48-2.840.1821420.148310151X-RAY DIFFRACTION99.99
2.84-3.570.17131400.158210083X-RAY DIFFRACTION99.96
3.57-46.860.18251440.142610144X-RAY DIFFRACTION99.91

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