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- PDB-7t89: Light harvesting complex Phycocyanin PC577 from the cryptophyte H... -

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Basic information

Entry
Database: PDB / ID: 7t89
TitleLight harvesting complex Phycocyanin PC577 from the cryptophyte Hemiselmis pacifica CCMP 706
Components
  • Phycoerythrin alpha subunit 1
  • Phycoerythrin beta subunit
KeywordsPHOTOSYNTHESIS / photosynthesis light harvesting
Function / homology
Function and homology information


phycobilisome / plastid / chloroplast thylakoid membrane / photosynthesis
Similarity search - Function
Phycoerythrin alpha chain / Phycoerythrin-like alpha chain superfamily / Phycoerythrin, alpha/beta chain / Globular protein, non-globular alpha/beta subunit / Phycobilisome, alpha/beta subunit / Phycobilisome, alpha/beta subunit superfamily / Phycobilisome protein / Globin-like superfamily
Similarity search - Domain/homology
DiCys-(15,16)-Dihydrobiliverdin / PHYCOCYANOBILIN / Phycoerythrin alpha subunit 1 / Phycoerythrin beta subunit
Similarity search - Component
Biological speciesHemiselmis pacifica (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1 Å
AuthorsMichie, K.A. / Curmi, P.C. / Harrop, S. / Rathbone, H.W.
Funding support Australia, United States, 3items
OrganizationGrant numberCountry
Australian Research Council (ARC)ARC LIEF LE190100165 Australia
Australian Research Council (ARC)DP180103964 Australia
Other governmentFA2386-17-1-4101 United States
Citation
Journal: Protein Sci. / Year: 2023
Title: Molecular structures reveal the origin of spectral variation in cryptophyte light harvesting antenna proteins.
Authors: Michie, K.A. / Harrop, S.J. / Rathbone, H.W. / Wilk, K.E. / Teng, C.Y. / Hoef-Emden, K. / Hiller, R.G. / 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: Acta Crystallogr D Struct Biol / Year: 2019
Title: Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix.
Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty ...Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty / Robert D Oeffner / Billy K Poon / Michael G Prisant / Randy J Read / Jane S Richardson / David C Richardson / Massimo D Sammito / Oleg V Sobolev / Duncan H Stockwell / Thomas C Terwilliger / Alexandre G Urzhumtsev / Lizbeth L Videau / Christopher J Williams / Paul D Adams /
Abstract: Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological ...Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological processes and to develop new therapeutics against diseases. The overall structure-solution workflow is similar for these techniques, but nuances exist because the properties of the reduced experimental data are different. Software tools for structure determination should therefore be tailored for each method. Phenix is a comprehensive software package for macromolecular structure determination that handles data from any of these techniques. Tasks performed with Phenix include data-quality assessment, map improvement, model building, the validation/rebuilding/refinement cycle and deposition. Each tool caters to the type of experimental data. The design of Phenix emphasizes the automation of procedures, where possible, to minimize repetitive and time-consuming manual tasks, while default parameters are chosen to encourage best practice. A graphical user interface provides access to many command-line features of Phenix and streamlines the transition between programs, project tracking and re-running of previous tasks.
History
DepositionDec 16, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 15, 2023Provider: repository / Type: Initial release
Revision 1.1Mar 8, 2023Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.2Aug 9, 2023Group: Refinement description / Category: pdbx_initial_refinement_model
Item: _pdbx_initial_refinement_model.accession_code / _pdbx_initial_refinement_model.type
Revision 1.3Oct 25, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Phycoerythrin alpha subunit 1
B: Phycoerythrin beta subunit
C: Phycoerythrin alpha subunit 1
D: Phycoerythrin beta subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,48012
Polymers49,7714
Non-polymers4,7108
Water13,655758
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17510 Å2
ΔGint-158 kcal/mol
Surface area19440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.116, 95.322, 125.577
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Phycoerythrin alpha subunit 1 / Phycoerythrin alpha subunit 2 / Phycoerythrin alpha subunit 3


Mass: 6581.592 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Hemiselmis pacifica (eukaryote) / References: UniProt: A0A067XP79
#2: Protein Phycoerythrin beta subunit


Mass: 18303.785 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Hemiselmis pacifica (eukaryote) / References: UniProt: A0A067XP89
#3: Chemical
ChemComp-CYC / PHYCOCYANOBILIN


Mass: 588.694 Da / Num. of mol.: 6 / Source method: obtained synthetically / 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.: 2 / Source method: obtained synthetically / Formula: C33H40N4O6 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 758 / Source method: isolated from a natural source / Formula: H2O
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: 2.56 Å3/Da / Density % sol: 52.04 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: PEG 10K, 15-25% 100 mM HEPES, pH7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.953698 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 19, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.953698 Å / Relative weight: 1
ReflectionResolution: 1→22.28 Å / Num. obs: 253580 / % possible obs: 93.4 % / Redundancy: 4.6 % / Biso Wilson estimate: 8.69 Å2 / CC1/2: 0.993 / Rmerge(I) obs: 0.061 / Rpim(I) all: 0.049 / Rrim(I) all: 0.078 / Χ2: 0.97 / Net I/σ(I): 16.6
Reflection shellResolution: 1.02→1.04 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.372 / Num. unique obs: 7164 / CC1/2: 0.778 / Rpim(I) all: 0.33 / Χ2: 0.9 / % possible all: 58.1

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
Blu-Icedata collection
XDSdata reduction
MOSFLMversion 1.12.4data reduction
Aimlessversion 0.7.4data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4LMS

4lms


Resolution: 1→22.28 Å / SU ML: 0.0734 / Cross valid method: FREE R-VALUE / σ(F): 0.14 / Phase error: 12.3672
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1428 12707 5.02 %
Rwork0.1326 240530 -
obs0.1331 253237 93.03 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 12.47 Å2
Refinement stepCycle: LAST / Resolution: 1→22.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3389 0 344 758 4491
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00724926
X-RAY DIFFRACTIONf_angle_d1.27856794
X-RAY DIFFRACTIONf_chiral_restr0.0744668
X-RAY DIFFRACTIONf_plane_restr0.0076872
X-RAY DIFFRACTIONf_dihedral_angle_d18.1981888
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1-1.010.24662510.2534922X-RAY DIFFRACTION57.82
1.01-1.020.26383090.24365416X-RAY DIFFRACTION63.48
1.02-1.040.22683240.22365916X-RAY DIFFRACTION69.63
1.04-1.050.20793560.21156501X-RAY DIFFRACTION76.27
1.05-1.060.20843970.20327168X-RAY DIFFRACTION84.18
1.06-1.080.20894040.18817921X-RAY DIFFRACTION92.36
1.08-1.090.1824020.17198102X-RAY DIFFRACTION95.02
1.09-1.110.1814050.16818232X-RAY DIFFRACTION95.09
1.11-1.130.117384180.16078150X-RAY DIFFRACTION95.66
1.13-1.140.17554460.16758200X-RAY DIFFRACTION95.74
1.14-1.160.17974450.17568207X-RAY DIFFRACTION96.13
1.16-1.190.18424410.1768231X-RAY DIFFRACTION96.44
1.19-1.210.17894410.18268324X-RAY DIFFRACTION96.53
1.21-1.230.18254390.18068234X-RAY DIFFRACTION96.66
1.23-1.260.18854710.17928279X-RAY DIFFRACTION96.94
1.26-1.290.17164410.16928344X-RAY DIFFRACTION97.28
1.29-1.320.16314240.16148421X-RAY DIFFRACTION97.4
1.32-1.360.16054150.16018426X-RAY DIFFRACTION97.83
1.36-1.40.16054410.15988411X-RAY DIFFRACTION97.92
1.4-1.440.16024510.168434X-RAY DIFFRACTION98.06
1.44-1.490.15864330.15538466X-RAY DIFFRACTION98.23
1.49-1.550.15094400.1478569X-RAY DIFFRACTION98.8
1.55-1.620.14454640.1468496X-RAY DIFFRACTION98.85
1.62-1.710.15324530.14428565X-RAY DIFFRACTION99.2
1.71-1.820.15594680.14398620X-RAY DIFFRACTION99.43
1.82-1.960.14364680.158617X-RAY DIFFRACTION99.58
1.96-2.150.15044690.15338670X-RAY DIFFRACTION99.6
2.15-2.470.14454530.14078713X-RAY DIFFRACTION99.19
2.47-3.10.14884930.15198791X-RAY DIFFRACTION99.98
3.1-22.280.24544450.2379184X-RAY DIFFRACTION99.9

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