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- PDB-7s97: Structure of the Photoacclimated Light Harvesting Complex PC577 f... -

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Basic information

Entry
Database: PDB / ID: 7s97
TitleStructure of the Photoacclimated Light Harvesting Complex PC577 from Hemiselmis pacifica
Components
  • Phycoerythrin alpha subunit 1
  • Phycoerythrin beta subunit
KeywordsPHOTOSYNTHESIS / phycobiliprotein / thylakoid lumen
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 / Phycocyanins / Phycobilisome, alpha/beta subunit / Phycobilisome, alpha/beta subunit superfamily / Phycobilisome protein / Globular protein, non-globular alpha/beta subunit / Globin-like / Globin-like superfamily ...Phycoerythrin alpha chain / Phycoerythrin-like alpha chain superfamily / Phycoerythrin, alpha/beta chain / Phycocyanins / Phycobilisome, alpha/beta subunit / Phycobilisome, alpha/beta subunit superfamily / Phycobilisome protein / Globular protein, non-globular alpha/beta subunit / Globin-like / Globin-like superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
PHYCOCYANOBILIN / 15,16-DIHYDROBILIVERDIN / Phycoerythrin alpha subunit 1 / Phycoerythrin beta subunit
Similarity search - Component
Biological speciesHemiselmis pacifica (eukaryote)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.35 Å
AuthorsJeffrey, P.D. / Spangler, L.C. / Scholes, G.D.
Funding support1items
OrganizationGrant numberCountry
Canadian Institute for Advanced Research
CitationJournal: Acs Cent.Sci. / Year: 2022
Title: Controllable Phycobilin Modification: An Alternative Photoacclimation Response in Cryptophyte Algae.
Authors: Spangler, L.C. / Yu, M. / Jeffrey, P.D. / Scholes, G.D.
History
DepositionSep 20, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 9, 2022Provider: repository / Type: Initial release
Revision 1.1Apr 20, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
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 subunit 1
B: Phycoerythrin beta subunit
C: Phycoerythrin alpha subunit 1
D: Phycoerythrin beta subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,00512
Polymers49,3044
Non-polymers4,7018
Water5,837324
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19500 Å2
ΔGint-184 kcal/mol
Surface area19070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.131, 95.736, 124.887
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 1 through 43 or resid 45 through 60 or resid 62 through 63 or resid 101))
21(chain C and (resid 1 through 43 or resid 45 through 60 or resid 62 through 63 or resid 101))
12(chain B and (resid 2 through 48 or resid 50...
22(chain D and ((resid 2 and (name N or name...

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111ALAALAMETMET(chain A and (resid 1 through 43 or resid 45 through 60 or resid 62 through 63 or resid 101))AA1 - 431 - 43
121LYSLYSTYRTYR(chain A and (resid 1 through 43 or resid 45 through 60 or resid 62 through 63 or resid 101))AA45 - 6045 - 60
131ASNASNALAALA(chain A and (resid 1 through 43 or resid 45 through 60 or resid 62 through 63 or resid 101))AA62 - 6362 - 63
141CYCCYCCYCCYC(chain A and (resid 1 through 43 or resid 45 through 60 or resid 62 through 63 or resid 101))AE101
211ALAALAMETMET(chain C and (resid 1 through 43 or resid 45 through 60 or resid 62 through 63 or resid 101))CC1 - 431 - 43
221LYSLYSTYRTYR(chain C and (resid 1 through 43 or resid 45 through 60 or resid 62 through 63 or resid 101))CC45 - 6045 - 60
231ASNASNALAALA(chain C and (resid 1 through 43 or resid 45 through 60 or resid 62 through 63 or resid 101))CC62 - 6362 - 63
241CYCCYCCYCCYC(chain C and (resid 1 through 43 or resid 45 through 60 or resid 62 through 63 or resid 101))CI101
112LEULEUALAALA(chain B and (resid 2 through 48 or resid 50...BB2 - 481 - 47
122CYSCYSVALVAL(chain B and (resid 2 through 48 or resid 50...BB50 - 5249 - 51
132LEULEUALAALA(chain B and (resid 2 through 48 or resid 50...BB2 - 1771 - 176
142LEULEUALAALA(chain B and (resid 2 through 48 or resid 50...BB2 - 1771 - 176
152LYSLYSALAALA(chain B and (resid 2 through 48 or resid 50...BB150 - 177149 - 176
162DBVDBVCYCCYC(chain B and (resid 2 through 48 or resid 50...BF - H201 - 203
212LEULEULEULEU(chain D and ((resid 2 and (name N or name...DD21
222LEULEUALAALA(chain D and ((resid 2 and (name N or name...DD2 - 1771 - 176
232LEULEUALAALA(chain D and ((resid 2 and (name N or name...DD2 - 1771 - 176
242LEULEUALAALA(chain D and ((resid 2 and (name N or name...DD2 - 1771 - 176
252LEULEUALAALA(chain D and ((resid 2 and (name N or name...DD2 - 1771 - 176

NCS ensembles :
ID
1
2

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Components

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


Mass: 6465.388 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: 18186.617 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-DBV / 15,16-DIHYDROBILIVERDIN


Mass: 584.662 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C33H36N4O6 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 324 / Source method: isolated from a natural source / Formula: H2O
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: 2.49 Å3/Da / Density % sol: 50.67 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 25% 3350 PEG, 50 mM HEPES, 100 mM MgCl2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: DECTRIS PILATUS3 R 300K / Detector: PIXEL / Date: Jul 2, 2021
RadiationMonochromator: Osmic optics / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.35→30 Å / Num. obs: 20796 / % possible obs: 97.5 % / Redundancy: 4.3 % / Rmerge(I) obs: 0.159 / Rpim(I) all: 0.081 / Rrim(I) all: 0.18 / Χ2: 1.14 / Net I/σ(I): 4.8 / Num. measured all: 90326
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.35-2.3930.7769910.6960.4920.9260.67295
2.39-2.4330.68710110.7660.4240.8140.63595.9
2.43-2.4830.569960.8490.3470.6640.67596.7
2.48-2.5330.5410260.80.3360.6420.62597.1
2.53-2.593.10.52310230.8280.3240.620.65297.2
2.59-2.653.20.4719970.8850.2850.5550.7297.4
2.65-2.713.30.51910220.8610.3110.6090.72797.1
2.71-2.793.40.4610340.9070.2750.540.75197.5
2.79-2.873.60.41510120.920.240.4820.77597.6
2.87-2.963.70.37910270.9180.2190.4410.90996.4
2.96-3.073.80.33710220.9450.1850.3870.98297.2
3.07-3.193.90.26610310.9250.1480.3071.15296.7
3.19-3.334.10.20210110.9510.1090.2311.29496.7
3.33-3.514.30.17710410.9510.0940.2021.4397.8
3.51-3.734.20.14410530.9680.0780.1641.55597.3
3.73-4.024.60.12910370.9840.0640.1451.40398
4.02-4.426.10.11910690.9910.0520.1311.67299.3
4.42-5.066.80.10411040.9930.0420.1121.2799.5
5.06-6.367.70.09510950.9960.0360.1021.06799.5
6.36-307.80.06511940.9980.0240.0691.48899.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
PHENIX1.17_3644refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7S96

7s96


Resolution: 2.35→29.68 Å / SU ML: 0.3 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 26.17 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2569 1050 5.06 %
Rwork0.1858 19685 -
obs0.1895 20735 97.27 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 86.59 Å2 / Biso mean: 28.2862 Å2 / Biso min: 10.45 Å2
Refinement stepCycle: final / Resolution: 2.35→29.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3431 0 344 324 4099
Biso mean--25.85 28.32 -
Num. residues----478
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073866
X-RAY DIFFRACTIONf_angle_d0.9115259
X-RAY DIFFRACTIONf_dihedral_angle_d13.6181394
X-RAY DIFFRACTIONf_chiral_restr0.049555
X-RAY DIFFRACTIONf_plane_restr0.005664
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A561X-RAY DIFFRACTION6.352TORSIONAL
12C561X-RAY DIFFRACTION6.352TORSIONAL
21B1563X-RAY DIFFRACTION6.352TORSIONAL
22D1563X-RAY DIFFRACTION6.352TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.35-2.470.32841380.21712682282094
2.47-2.630.32111430.21762757290097
2.63-2.830.29311360.22542773290997
2.83-3.120.28291560.22192783293997
3.12-3.570.24671350.17542808294397
3.57-4.490.23341810.15742836301798
4.49-29.680.21871610.166530463207100

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