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- PDB-8el5: Light harvesting phycobiliprotein HaPE555 from the cryptophyte He... -

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Basic information

Entry
Database: PDB / ID: 8el5
TitleLight harvesting phycobiliprotein HaPE555 from the cryptophyte Hemiselmis andersenii CCMP644 in an alternating tight to 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: 1.67 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)140,54538
Polymers128,21812
Non-polymers12,32626
Water6,107339
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)70,18018
Polymers64,1096
Non-polymers6,07112
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)70,36520
Polymers64,1096
Non-polymers6,25514
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)64.856, 75.596, 99.360
Angle α, β, γ (deg.)90.000, 110.304, 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 , 4 types, 365 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: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 339 / 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: 1.78 Å3/Da / Density % sol: 30.96 %
Crystal growTemperature: 300 K / Method: vapor diffusion, sitting drop
Details: 25% PEG3350 (w/v) + 2% (w/v) Benzamidine HCl, 150 nL mother + 150 nl protein solution, Cryoprotectant of 20% Gylcerol

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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: 1.67→61.7 Å / Num. obs: 104433 / % possible obs: 100 % / Redundancy: 6.7 % / Biso Wilson estimate: 28 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.091 / Net I/σ(I): 9.5
Reflection shellResolution: 1.67→1.7 Å / Mean I/σ(I) obs: 0.7 / Num. unique obs: 5125 / CC1/2: 0.406

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
Coot0.95model building
DIALSdata reduction
Aimless0.7.7data scaling
PHENIX1.14phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4LMX

4lmx


Resolution: 1.67→61.66 Å / SU ML: 0.2914 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 28.6129
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2314 1998 1.92 %
Rwork0.1858 102109 -
obs0.1866 104107 99.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 39.11 Å2
Refinement stepCycle: LAST / Resolution: 1.67→61.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8713 0 896 339 9948
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.013110003
X-RAY DIFFRACTIONf_angle_d1.446413578
X-RAY DIFFRACTIONf_chiral_restr0.06331456
X-RAY DIFFRACTIONf_plane_restr0.00921722
X-RAY DIFFRACTIONf_dihedral_angle_d17.10473640
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.67-1.710.48991400.4097177X-RAY DIFFRACTION98.24
1.71-1.760.36531510.35297226X-RAY DIFFRACTION99.45
1.76-1.810.34721390.31227269X-RAY DIFFRACTION99.64
1.81-1.870.33671430.27297230X-RAY DIFFRACTION99.81
1.87-1.930.29511440.24847284X-RAY DIFFRACTION99.77
1.93-2.010.30341350.23787264X-RAY DIFFRACTION99.78
2.01-2.10.29191450.20167295X-RAY DIFFRACTION99.84
2.1-2.210.23331400.18547297X-RAY DIFFRACTION99.92
2.22-2.350.22291430.18297289X-RAY DIFFRACTION99.96
2.35-2.540.22391410.17987299X-RAY DIFFRACTION99.97
2.54-2.790.23491450.17877342X-RAY DIFFRACTION99.93
2.79-3.190.25111420.17457331X-RAY DIFFRACTION99.95
3.19-4.020.21881430.15837375X-RAY DIFFRACTION99.97
4.03-61.660.17051470.15877431X-RAY DIFFRACTION99.4

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