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- PDB-8el3: Light harvesting phycobiliprotein HaPE555 from the cryptophyte He... -

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Basic information

Entry
Database: PDB / ID: 8el3
TitleLight harvesting phycobiliprotein HaPE555 from the cryptophyte Hemiselmis andersenii CCMP644 in a loose interface filament
Components
  • (Phycoerythrin alpha- ...) x 2
  • Phycoerythrin550 beta subunit
KeywordsPHOTOSYNTHESIS / phycobiliprotein / antenna / light harvesting / cryptophyte / algae / globin / CALM / CaRSP / phycoerythrin / Hemiselmis
Function / homology
Function and homology information


phycobilisome / chloroplast thylakoid membrane / photosynthesis
Similarity search - Function
Phycoerythrin alpha chain / Phycoerythrin-like alpha chain superfamily / Phycoerythrin, alpha/beta chain / Phycobilisome, alpha/beta subunit / Phycobilisome, alpha/beta subunit superfamily / Phycobilisome protein / Globular protein, non-globular alpha/beta subunit / Globin-like superfamily
Similarity search - Domain/homology
DiCys-(15,16)-Dihydrobiliverdin / PHYCOERYTHROBILIN / Phycoerythrin beta subunit / Phycoerythrin alpha-2 subunit / Phycoerythrin alpha-1 subunit
Similarity search - Component
Biological speciesHemiselmis andersenii (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.57 Å
AuthorsRathbone, H.W. / Michie, K.A. / Laos, A.L. / Curmi, P.M.G.
Funding support Australia, 3items
OrganizationGrant numberCountry
Australian Research Council (ARC)DP180103964 Australia
Other governmentFA2386-17-1-4101 (U.S. Air Force Office of Scientific Research through the Asian Office of Aerospace Research and Developmen)
Australian Research Council (ARC)LE190100165 Australia
CitationJournal: Commun Biol / Year: 2023
Title: Molecular dissection of the soluble photosynthetic antenna from the cryptophyte alga Hemiselmis andersenii.
Authors: Rathbone, H.W. / Laos, A.J. / Michie, K.A. / Iranmanesh, H. / Biazik, J. / Goodchild, S.C. / Thordarson, P. / Green, B.R. / Curmi, P.M.G.
History
DepositionSep 23, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 25, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2023Group: Database references / Category: citation / Item: _citation.pdbx_database_id_DOI
Revision 1.2Nov 29, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.3Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Phycoerythrin alpha-1 subunit
B: Phycoerythrin550 beta subunit
C: Phycoerythrin alpha-2 subunit
D: Phycoerythrin550 beta subunit
E: Phycoerythrin alpha-2 subunit
F: Phycoerythrin550 beta subunit
G: Phycoerythrin alpha-1 subunit
H: Phycoerythrin550 beta subunit
I: Phycoerythrin alpha-2 subunit
J: Phycoerythrin alpha-1 subunit
K: Phycoerythrin alpha-1 subunit
L: Phycoerythrin alpha-2 subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)139,99232
Polymers128,21812
Non-polymers11,77420
Water12,520695
1
A: Phycoerythrin alpha-1 subunit
B: Phycoerythrin550 beta subunit
C: Phycoerythrin alpha-2 subunit
D: Phycoerythrin550 beta subunit
I: Phycoerythrin alpha-2 subunit
J: Phycoerythrin alpha-1 subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,99616
Polymers64,1096
Non-polymers5,88710
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
E: Phycoerythrin alpha-2 subunit
F: Phycoerythrin550 beta subunit
G: Phycoerythrin alpha-1 subunit
H: Phycoerythrin550 beta subunit
K: Phycoerythrin alpha-1 subunit
L: Phycoerythrin alpha-2 subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,99616
Polymers64,1096
Non-polymers5,88710
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)64.802, 76.840, 103.360
Angle α, β, γ (deg.)90.000, 110.732, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

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Phycoerythrin alpha- ... , 2 types, 8 molecules AGJKCEIL

#1: Protein
Phycoerythrin alpha-1 subunit / Phycoerythrin PE555 alpha-1 subunit / PE555A-1


Mass: 7019.024 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Hemiselmis andersenii (eukaryote) / References: UniProt: U5TBU5
#3: Protein
Phycoerythrin alpha-2 subunit / Phycoerythrin PE555 alpha-2 subunit / PE555A-2


Mass: 6628.628 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Hemiselmis andersenii (eukaryote) / References: UniProt: U5TBJ3

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Protein , 1 types, 4 molecules BDFH

#2: Protein
Phycoerythrin550 beta subunit


Mass: 18406.949 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Hemiselmis andersenii (eukaryote) / References: UniProt: U5T8W0

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Non-polymers , 3 types, 715 molecules

#4: Chemical
ChemComp-PEB / PHYCOERYTHROBILIN


Mass: 588.694 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C33H40N4O6
#5: Chemical
ChemComp-AX9 / DiCys-(15,16)-Dihydrobiliverdin / 15,16-DIHYDROBILIVERDIN (double Cys bound form) / 3-[(2Z)-2-({3-(2-carboxyethyl)-5-[(Z)-(3-ethyl-4-methyl-5-oxo-1,5-dihydro-2H-pyrrol-2-ylidene)methyl]-4-methyl-1H-pyrrol-2-yl}methylidene)-5-{[(2R)-4-ethyl-3-methyl-5-oxo-2,5-dihydro-1H-pyrrol-2-yl]methyl}-4-methyl-2H-pyrrol-3-yl]propanoic acid


Mass: 588.694 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C33H40N4O6
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 695 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
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: 1.88 Å3/Da / Density % sol: 34.47 %
Crystal growTemperature: 300 K / Method: vapor diffusion, sitting drop
Details: PEG3350 25% (w/v) + NaBr 0.01M, 150nL mother + 150 nL protein stock, Cryoprotectant of 20% Glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 16, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.57→48.33 Å / Num. obs: 129756 / % possible obs: 98.2 % / Redundancy: 6.4 % / Biso Wilson estimate: 19.58 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.095 / Net I/σ(I): 10.5
Reflection shellResolution: 1.57→1.6 Å / Rmerge(I) obs: 1.399 / Mean I/σ(I) obs: 1 / Num. unique obs: 5326 / CC1/2: 0.4

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
Coot0.9.5model building
DIALSdata reduction
Aimless0.7.7data scaling
PHENIX1.14phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4LMX

4lmx


Resolution: 1.57→48.33 Å / SU ML: 0.2128 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 20.8129
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.201 1989 1.53 %
Rwork0.1701 127629 -
obs0.1706 129618 98.03 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 23.34 Å2
Refinement stepCycle: LAST / Resolution: 1.57→48.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8737 0 860 695 10292
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012910016
X-RAY DIFFRACTIONf_angle_d1.384913610
X-RAY DIFFRACTIONf_chiral_restr0.06171462
X-RAY DIFFRACTIONf_plane_restr0.00881732
X-RAY DIFFRACTIONf_dihedral_angle_d16.26883646
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.57-1.610.37821220.34447603X-RAY DIFFRACTION82.46
1.61-1.650.29981360.29768683X-RAY DIFFRACTION93.49
1.65-1.70.26961370.24949098X-RAY DIFFRACTION98.19
1.7-1.760.27121470.21489212X-RAY DIFFRACTION99.45
1.76-1.820.22121400.19779188X-RAY DIFFRACTION99.62
1.82-1.890.22671460.17959280X-RAY DIFFRACTION99.82
1.89-1.980.21431400.17949275X-RAY DIFFRACTION99.84
1.98-2.080.20591550.18539247X-RAY DIFFRACTION99.88
2.08-2.210.18631430.15249283X-RAY DIFFRACTION99.93
2.21-2.380.19131430.15129309X-RAY DIFFRACTION99.99
2.38-2.620.18571430.15229283X-RAY DIFFRACTION100
2.62-30.19541450.15879317X-RAY DIFFRACTION99.96
3-3.780.17571470.15299379X-RAY DIFFRACTION99.99
3.78-48.330.18831450.1599472X-RAY DIFFRACTION99.71

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