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- PDB-7ssf: Light harvesting phycobiliprotein HaPE560 from the cryptophyte He... -

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Basic information

Entry
Database: PDB / ID: 7ssf
TitleLight harvesting phycobiliprotein HaPE560 from the cryptophyte Hemiselmis andersenii CCMP644
Components
  • HaPE560 alpha subunit
  • 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
Phycobilisome, alpha/beta subunit / Phycobilisome, alpha/beta subunit superfamily / Phycobilisome protein / Globin-like superfamily
Similarity search - Domain/homology
DiCys-(15,16)-Dihydrobiliverdin / PHYCOERYTHROBILIN / Phycoerythrin beta subunit
Similarity search - Component
Biological speciesHemiselmis andersenii (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 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. / Curmi, P.M.G. / Michie, K.A. / Green, B.R. / Laos, A.L. / Thordarson, P. / Iranmanesh, H.
#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: 2015
Title: MX1: a bending-magnet crystallography beamline serving both chemical and macromolecular crystallography communities at the Australian Synchrotron.
Authors: Cowieson, N.P. / Aragao, D. / Clift, M. / Ericsson, D.J. / Gee, C. / Harrop, S.J. / Mudie, N. / Panjikar, S. / Price, J.R. / Riboldi-Tunnicliffe, A. / Williamson, R. / Caradoc-Davies, T.
#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.
History
DepositionNov 10, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 25, 2023Provider: repository / Type: Initial release
Revision 2.0Nov 15, 2023Group: Atomic model / Database references / Category: atom_site / citation
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.label_alt_id / _atom_site.label_atom_id / _atom_site.occupancy / _citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HaPE560 alpha subunit
B: Phycoerythrin550 beta subunit
C: HaPE560 alpha subunit
D: Phycoerythrin550 beta subunit
E: HaPE560 alpha subunit
F: Phycoerythrin550 beta subunit
G: HaPE560 alpha subunit
H: Phycoerythrin550 beta subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,30428
Polymers104,4838
Non-polymers9,82120
Water14,646813
1
A: HaPE560 alpha subunit
B: Phycoerythrin550 beta subunit
C: HaPE560 alpha subunit
D: Phycoerythrin550 beta subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,07313
Polymers52,2414
Non-polymers4,8329
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
E: HaPE560 alpha subunit
F: Phycoerythrin550 beta subunit
G: HaPE560 alpha subunit
H: Phycoerythrin550 beta subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,23115
Polymers52,2414
Non-polymers4,98911
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)84.320, 67.970, 184.494
Angle α, β, γ (deg.)90.000, 99.330, 90.000
Int Tables number5
Space group name H-MI121
Space group name HallC2y(x,y,-x+z)
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z+1/2
#4: -x+1/2,y+1/2,-z+1/2
Components on special symmetry positions
IDModelComponents
11F-386-

HOH

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Components

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Protein , 2 types, 8 molecules ACEGBDFH

#1: Protein
HaPE560 alpha subunit


Mass: 7713.771 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Hemiselmis andersenii (eukaryote) / Strain: CCMP644
#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 , 5 types, 833 molecules

#3: Chemical
ChemComp-PEB / PHYCOERYTHROBILIN


Mass: 588.694 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Formula: C33H40N4O6 / Feature type: SUBJECT OF INVESTIGATION
#4: 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
#5: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#6: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 813 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.53 Å3/Da / Density % sol: 51.34 %
Crystal growTemperature: 300 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: TRIS HCl 0.162 M + PEGMME 5000 21.4 % (v/v)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Feb 23, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.45→28.94 Å / Num. obs: 181639 / % possible obs: 99.8 % / Redundancy: 7.4 % / Biso Wilson estimate: 14.93 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.095 / Net I/σ(I): 12.5
Reflection shellResolution: 1.45→1.47 Å / Redundancy: 7.2 % / Rmerge(I) obs: 1.424 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 8893 / CC1/2: 0.546 / % possible all: 99.3

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
iMOSFLMdata reduction
pointless1.11.17data scaling
Aimless0.7.3data scaling
PHENIX1.14phasing
Coot0.9.5model building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4LMX

4lmx


Resolution: 1.45→28.94 Å / SU ML: 0.1588 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.0252
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1921 9097 5.01 %
Rwork0.1541 172526 -
obs0.156 181623 99.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 23.87 Å2
Refinement stepCycle: LAST / Resolution: 1.45→28.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7195 0 713 813 8721
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01278776
X-RAY DIFFRACTIONf_angle_d1.415111992
X-RAY DIFFRACTIONf_chiral_restr0.07131237
X-RAY DIFFRACTIONf_plane_restr0.00951555
X-RAY DIFFRACTIONf_dihedral_angle_d15.91673271
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.45-1.470.29953170.27735720X-RAY DIFFRACTION99.39
1.47-1.480.29013190.24895686X-RAY DIFFRACTION99.39
1.48-1.50.29192970.23785694X-RAY DIFFRACTION99.49
1.5-1.520.27482810.22055674X-RAY DIFFRACTION99.28
1.52-1.540.26473260.2095697X-RAY DIFFRACTION99.5
1.54-1.560.24023140.19635704X-RAY DIFFRACTION99.42
1.56-1.580.22662920.18435729X-RAY DIFFRACTION99.67
1.58-1.610.23882950.17775715X-RAY DIFFRACTION99.5
1.61-1.630.25522730.18475737X-RAY DIFFRACTION99.73
1.63-1.660.2152990.17545783X-RAY DIFFRACTION99.77
1.66-1.690.20283130.16715647X-RAY DIFFRACTION99.83
1.69-1.720.20492950.1625833X-RAY DIFFRACTION99.85
1.72-1.750.22412840.16145693X-RAY DIFFRACTION99.98
1.75-1.790.21773000.15975773X-RAY DIFFRACTION99.97
1.79-1.830.19683060.14895734X-RAY DIFFRACTION100
1.83-1.870.19483370.14575750X-RAY DIFFRACTION100
1.87-1.920.2012840.14855731X-RAY DIFFRACTION99.98
1.92-1.970.19143330.14485731X-RAY DIFFRACTION99.95
1.97-2.030.18743140.14615766X-RAY DIFFRACTION99.97
2.03-2.090.20082860.14645738X-RAY DIFFRACTION99.93
2.09-2.170.18182940.13955806X-RAY DIFFRACTION99.92
2.17-2.250.17763310.13945748X-RAY DIFFRACTION99.92
2.25-2.350.18283050.14045768X-RAY DIFFRACTION100
2.36-2.480.16663110.1345714X-RAY DIFFRACTION100
2.48-2.630.16982870.13955829X-RAY DIFFRACTION99.93
2.63-2.840.18093100.14535781X-RAY DIFFRACTION99.92
2.84-3.120.18282810.15435816X-RAY DIFFRACTION99.93
3.12-3.570.19983390.15825784X-RAY DIFFRACTION99.93
3.57-4.50.16512930.13985848X-RAY DIFFRACTION99.9
4.5-28.940.15992810.14775897X-RAY DIFFRACTION98.82

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