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- PDB-7sut: Light harvesting phycobiliprotein HaPE645 from the cryptophyte He... -

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Basic information

Entry
Database: PDB / ID: 7sut
TitleLight harvesting phycobiliprotein HaPE645 from the cryptophyte Hemiselmis andersenii CCMP644
Components
  • (HaPE645 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 / PHYCOCYANOBILIN / PHYCOERYTHROBILIN / (15,16)-DIHYDROBILIVERDIN (SINGLY LINKED) / Phycoerythrin alpha chain domain-containing protein / Phycoerythrin beta subunit
Similarity search - Component
Biological speciesHemiselmis andersenii (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.49 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) Australia
Australian Research Council (ARC)LE190100165 Australia
Citation
Journal: 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.
#1: Journal: Acta Crystallogr D Biol Crystallogr / Year: 2012
Title: Towards automated crystallographic structure refinement with phenix.refine.
Authors: Afonine, P.V. / Grosse-Kunstleve, R.W. / Echols, N. / Headd, J.J. / Moriarty, N.W. / Mustyakimov, M. / Terwilliger, T.C. / Urzhumtsev, A. / Zwart, P.H. / Adams, P.D.
#2: Journal: J Synchrotron Radiat / Year: 2002
Title: Blu-Ice and the Distributed Control System: software for data acquisition and instrument control at macromolecular crystallography beamlines.
Authors: McPhillips, T.M. / McPhillips, S.E. / Chiu, H.J. / Cohen, A.E. / Deacon, A.M. / Ellis, P.J. / Garman, E. / Gonzalez, A. / Sauter, N.K. / Phizackerley, R.P. / Soltis, S.M. / Kuhn, P.
#3: Journal: Acta Crystallogr D Biol Crystallogr / Year: 2004
Title: Coot: model-building tools for molecular graphics.
Authors: Emsley, P. / Cowtan, K.
#4: Journal: Acta Crystallogr D Biol Crystallogr / Year: 2011
Title: Overview of the CCP4 suite and current developments.
Authors: Winn, M.D. / Ballard, C.C. / Cowtan, K.D. / Dodson, E.J. / Emsley, P. / Evans, P.R. / Keegan, R.M. / Krissinel, E.B. / Leslie, A.G. / McCoy, A. / McNicholas, S.J. / Murshudov, G.N. / Pannu, ...Authors: Winn, M.D. / Ballard, C.C. / Cowtan, K.D. / Dodson, E.J. / Emsley, P. / Evans, P.R. / Keegan, R.M. / Krissinel, E.B. / Leslie, A.G. / McCoy, A. / McNicholas, S.J. / Murshudov, G.N. / Pannu, N.S. / Potterton, E.A. / Powell, H.R. / Read, R.J. / Vagin, A. / Wilson, K.S.
#5: Journal: J Appl Crystallogr / Year: 2007
Title: Phaser crystallographic software.
Authors: McCoy, A.J. / Grosse-Kunstleve, R.W. / Adams, P.D. / Winn, M.D. / Storoni, L.C. / Read, R.J.
#6: Journal: J Synchrotron Radiat / Year: 2018
Title: MX2: a high-flux undulator microfocus beamline serving both the chemical and macromolecular crystallography communities at the Australian Synchrotron.
Authors: Aragao, D. / Aishima, J. / Cherukuvada, H. / Clarken, R. / Clift, M. / Cowieson, N.P. / Ericsson, D.J. / Gee, C.L. / Macedo, S. / Mudie, N. / Panjikar, S. / Price, J.R. / Riboldi- ...Authors: Aragao, D. / Aishima, J. / Cherukuvada, H. / Clarken, R. / Clift, M. / Cowieson, N.P. / Ericsson, D.J. / Gee, C.L. / Macedo, S. / Mudie, N. / Panjikar, S. / Price, J.R. / Riboldi-Tunnicliffe, A. / Rostan, R. / Williamson, R. / Caradoc-Davies, T.T.
History
DepositionNov 18, 2021Deposition 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.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.year
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: HaPE645 alpha-1 subunit
B: Phycoerythrin550 beta subunit
C: HaPE645 alpha-2 subunit
D: Phycoerythrin550 beta subunit
E: HaPE645 alpha-1 subunit
F: Phycoerythrin550 beta subunit
G: HaPE645 alpha-2 subunit
H: Phycoerythrin550 beta subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)117,22028
Polymers107,1688
Non-polymers10,05220
Water8,215456
1
A: HaPE645 alpha-1 subunit
B: Phycoerythrin550 beta subunit
C: HaPE645 alpha-2 subunit
D: Phycoerythrin550 beta subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,73215
Polymers53,5844
Non-polymers5,14811
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area22210 Å2
ΔGint-167 kcal/mol
Surface area17630 Å2
MethodPISA
2
E: HaPE645 alpha-1 subunit
F: Phycoerythrin550 beta subunit
G: HaPE645 alpha-2 subunit
H: Phycoerythrin550 beta subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,48813
Polymers53,5844
Non-polymers4,9049
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area21610 Å2
ΔGint-160 kcal/mol
Surface area17580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.032, 80.983, 115.837
Angle α, β, γ (deg.)90.000, 92.214, 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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HaPE645 alpha- ... , 2 types, 4 molecules AECG

#1: Protein HaPE645 alpha-1 subunit


Mass: 8974.020 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Hemiselmis andersenii (eukaryote) / References: UniProt: A0A7S0U215
#3: Protein HaPE645 alpha-2 subunit


Mass: 7795.986 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Hemiselmis andersenii (eukaryote) / Strain: CCMP644

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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 , 8 types, 476 molecules

#4: Chemical
ChemComp-X2I / (15,16)-DIHYDROBILIVERDIN (SINGLY LINKED) / 3-(2-{[3-(2-carboxyethyl)-5-{[(2R)-4-ethenyl-3-methyl-5-oxo-2,5-dihydro-1H-pyrrol-2-yl]methyl}-4-methyl-1H-pyrrol-2-yl]methyl}-5-[(Z)-(3-ethyl-4-methyl-5-oxo-1,5-dihydro-2H-pyrrol-2-ylidene)methyl]-4-methyl-1H-pyrrol-3-yl)propanoic acid


Mass: 588.694 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C33H40N4O6 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#6: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#7: 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 / Feature type: SUBJECT OF INVESTIGATION
#8: Chemical
ChemComp-PEB / PHYCOERYTHROBILIN


Mass: 588.694 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C33H40N4O6 / Feature type: SUBJECT OF INVESTIGATION
#9: Chemical ChemComp-BTB / 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / BIS-TRIS BUFFER


Mass: 209.240 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H19NO5 / Comment: pH buffer*YM
#10: Chemical ChemComp-CYC / PHYCOCYANOBILIN


Mass: 588.694 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C33H40N4O6 / Feature type: SUBJECT OF INVESTIGATION
#11: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 456 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
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: 2.36 Å3/Da / Density % sol: 47.95 %
Crystal growTemperature: 300 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: 0.1 M Bis-Tris + 25 % (w/v) PEG 3350

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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: Feb 28, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.49→115.75 Å / Num. obs: 151716 / % possible obs: 93.4 % / Redundancy: 3.6 % / Biso Wilson estimate: 19.89 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.056 / Net I/σ(I): 9.9
Reflection shellResolution: 1.49→1.52 Å / Redundancy: 2.2 % / Rmerge(I) obs: 1.117 / Mean I/σ(I) obs: 0.9 / Num. unique obs: 4645 / CC1/2: 0.463 / % possible all: 58.3

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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: 1.49→41.43 Å / SU ML: 0.1629 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 18.3653
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1747 1871 1.23 %
Rwork0.1455 149795 -
obs0.1459 151666 93.28 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 26.94 Å2
Refinement stepCycle: LAST / Resolution: 1.49→41.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7100 0 729 456 8285
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01068369
X-RAY DIFFRACTIONf_angle_d1.316511402
X-RAY DIFFRACTIONf_chiral_restr0.07321192
X-RAY DIFFRACTIONf_plane_restr0.00811451
X-RAY DIFFRACTIONf_dihedral_angle_d17.53343129
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.49-1.530.3355920.28967376X-RAY DIFFRACTION59.84
1.53-1.580.29521040.24158831X-RAY DIFFRACTION71.81
1.58-1.630.281350.208810604X-RAY DIFFRACTION86.04
1.63-1.680.22811460.179911945X-RAY DIFFRACTION96.72
1.68-1.750.20251490.162612226X-RAY DIFFRACTION99.64
1.75-1.830.21181570.166912267X-RAY DIFFRACTION99.74
1.83-1.930.2061610.141412319X-RAY DIFFRACTION99.77
1.93-2.050.1781570.12412264X-RAY DIFFRACTION99.91
2.05-2.210.15931450.119812349X-RAY DIFFRACTION99.82
2.21-2.430.14891570.115812329X-RAY DIFFRACTION99.71
2.43-2.780.17431570.123912364X-RAY DIFFRACTION99.9
2.78-3.50.16771580.143712362X-RAY DIFFRACTION99.75
3.5-41.430.1531530.15512559X-RAY DIFFRACTION99.79

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