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- PDB-6zid: Ultrafast Structural Response to Charge Redistribution Within a P... -

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Basic information

Entry
Database: PDB / ID: 6zid
TitleUltrafast Structural Response to Charge Redistribution Within a Photosynthetic Reaction Centre - 5 ps (b) structure
Components
  • (Reaction center protein ...) x 3
  • Photosynthetic reaction center cytochrome c subunit
KeywordsELECTRON TRANSPORT / ELECTRON TRANSPORT Photosynthesis Membrane Protein
Function / homology
Function and homology information


plasma membrane-derived chromatophore membrane / plasma membrane light-harvesting complex / bacteriochlorophyll binding / photosynthetic electron transport in photosystem II / : / photosynthesis, light reaction / photosynthesis / electron transfer activity / iron ion binding / heme binding / metal ion binding
Similarity search - Function
Photosynthetic reaction centre, cytochrome c subunit / Multihaem cytochrome, PRC subunit superfamily / Photosynthetic reaction centre cytochrome C subunit / Multiheme cytochrome c family profile. / Photosynthetic reaction centre, H subunit / Bacterial photosynthetic reaction centre, H-chain, C-terminal / Photosynthetic reaction centre, M subunit / Photosynthetic reaction centre, H subunit, N-terminal / PRC-barrel domain / Photosynthetic reaction centre, H subunit, N-terminal domain superfamily ...Photosynthetic reaction centre, cytochrome c subunit / Multihaem cytochrome, PRC subunit superfamily / Photosynthetic reaction centre cytochrome C subunit / Multiheme cytochrome c family profile. / Photosynthetic reaction centre, H subunit / Bacterial photosynthetic reaction centre, H-chain, C-terminal / Photosynthetic reaction centre, M subunit / Photosynthetic reaction centre, H subunit, N-terminal / PRC-barrel domain / Photosynthetic reaction centre, H subunit, N-terminal domain superfamily / Photosynthetic reaction centre, H-chain N-terminal region / PRC-barrel domain / Photosynthetic reaction centre, L subunit / PRC-barrel-like superfamily / Multiheme cytochrome superfamily / : / Photosynthetic reaction centre, L/M / Photosystem II protein D1/D2 superfamily / Photosynthetic reaction centre protein / Photosynthetic reaction center proteins signature. / Prokaryotic membrane lipoprotein lipid attachment site profile.
Similarity search - Domain/homology
BACTERIOCHLOROPHYLL B / BACTERIOPHEOPHYTIN B / DIACYL GLYCEROL / : / HEME C / HEPTANE-1,2,3-TRIOL / MENAQUINONE-7 / 15-cis-1,2-dihydroneurosporene / Reaction center protein H chain / Reaction center protein L chain ...BACTERIOCHLOROPHYLL B / BACTERIOPHEOPHYTIN B / DIACYL GLYCEROL / : / HEME C / HEPTANE-1,2,3-TRIOL / MENAQUINONE-7 / 15-cis-1,2-dihydroneurosporene / Reaction center protein H chain / Reaction center protein L chain / Reaction center protein M chain / Photosynthetic reaction center cytochrome c subunit
Similarity search - Component
Biological speciesBlastochloris viridis (bacteria)
MethodX-RAY DIFFRACTION / FREE ELECTRON LASER / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsBaath, P. / Dods, R. / Braenden, G. / Neutze, R.
Funding support United States, Sweden, Finland, 5items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P41GM103393 United States
Swedish Research Council2015-00560, 349-2011-6485, 2017-06734 Sweden
The Swedish Foundation for Strategic ResearchSRL10-0036 Sweden
Knut and Alice Wallenberg FoundationKAW 2012.0284, KAW 2014.0275 Sweden
Academy of Finland290677, 304455 Finland
CitationJournal: Nature / Year: 2021
Title: Ultrafast structural changes within a photosynthetic reaction centre.
Authors: Dods, R. / Bath, P. / Morozov, D. / Gagner, V.A. / Arnlund, D. / Luk, H.L. / Kubel, J. / Maj, M. / Vallejos, A. / Wickstrand, C. / Bosman, R. / Beyerlein, K.R. / Nelson, G. / Liang, M. / ...Authors: Dods, R. / Bath, P. / Morozov, D. / Gagner, V.A. / Arnlund, D. / Luk, H.L. / Kubel, J. / Maj, M. / Vallejos, A. / Wickstrand, C. / Bosman, R. / Beyerlein, K.R. / Nelson, G. / Liang, M. / Milathianaki, D. / Robinson, J. / Harimoorthy, R. / Berntsen, P. / Malmerberg, E. / Johansson, L. / Andersson, R. / Carbajo, S. / Claesson, E. / Conrad, C.E. / Dahl, P. / Hammarin, G. / Hunter, M.S. / Li, C. / Lisova, S. / Royant, A. / Safari, C. / Sharma, A. / Williams, G.J. / Yefanov, O. / Westenhoff, S. / Davidsson, J. / DePonte, D.P. / Boutet, S. / Barty, A. / Katona, G. / Groenhof, G. / Branden, G. / Neutze, R.
History
DepositionJun 25, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 9, 2020Provider: repository / Type: Initial release
Revision 1.1Dec 16, 2020Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Jan 27, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.3Dec 13, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_related_exp_data_set / pdbx_validate_chiral
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Jan 31, 2024Group: Refinement description / Category: pdbx_initial_refinement_model
Revision 1.5Nov 20, 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
C: Photosynthetic reaction center cytochrome c subunit
H: Reaction center protein H chain
L: Reaction center protein L chain
M: Reaction center protein M chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)145,65843
Polymers132,4104
Non-polymers13,24839
Water2,630146
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area54220 Å2
ΔGint-546 kcal/mol
Surface area42040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)226.500, 226.500, 113.900
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Space group name HallP4nw2abw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+3/4
#3: y+1/2,-x+1/2,z+1/4
#4: x+1/2,-y+1/2,-z+1/4
#5: -x+1/2,y+1/2,-z+3/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2
Components on special symmetry positions
IDModelComponents
11H-706-

SO4

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Components

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Protein , 1 types, 1 molecules C

#1: Protein Photosynthetic reaction center cytochrome c subunit / Cytochrome c558/c559


Mass: 37450.801 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Blastochloris viridis (bacteria) / References: UniProt: P07173

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Reaction center protein ... , 3 types, 3 molecules HLM

#2: Protein Reaction center protein H chain / Photosynthetic reaction center H subunit


Mass: 28557.453 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Blastochloris viridis (bacteria) / References: UniProt: P06008
#3: Protein Reaction center protein L chain / Photosynthetic reaction center L subunit


Mass: 30469.104 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Blastochloris viridis (bacteria) / References: UniProt: P06009
#4: Protein Reaction center protein M chain / Photosynthetic reaction center M subunit


Mass: 35932.188 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Blastochloris viridis (bacteria) / References: UniProt: P06010

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Non-polymers , 11 types, 185 molecules

#5: Chemical
ChemComp-HEC / HEME C


Mass: 618.503 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H34FeN4O4
#6: Chemical ChemComp-DGA / DIACYL GLYCEROL


Mass: 625.018 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C39H76O5
#7: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: SO4
#8: Chemical
ChemComp-LDA / LAURYL DIMETHYLAMINE-N-OXIDE


Mass: 229.402 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C14H31NO / Comment: LDAO, detergent*YM
#9: Chemical ChemComp-HTO / HEPTANE-1,2,3-TRIOL


Mass: 148.200 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C7H16O3
#10: Chemical
ChemComp-BCB / BACTERIOCHLOROPHYLL B


Mass: 909.488 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C55H72MgN4O6 / Feature type: SUBJECT OF INVESTIGATION
#11: Chemical ChemComp-BPB / BACTERIOPHEOPHYTIN B


Mass: 887.199 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C55H74N4O6 / Feature type: SUBJECT OF INVESTIGATION
#12: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#13: Chemical ChemComp-MQ7 / MENAQUINONE-7


Mass: 648.999 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C46H64O2 / Feature type: SUBJECT OF INVESTIGATION
#14: Chemical ChemComp-NS5 / 15-cis-1,2-dihydroneurosporene


Mass: 540.904 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C40H60
#15: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 146 / 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

Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: Macrocrystal growth: 10 mg/ml protein, 3.6 M ammonium sulphate, 6 % w/v heptane-1,2,3-triol, 20 mM KH203/K2H03 pH 6.8, 0.1 % LDAO 20 ul sitting drop, 10 protein : 10 precipitant ...Details: Macrocrystal growth: 10 mg/ml protein, 3.6 M ammonium sulphate, 6 % w/v heptane-1,2,3-triol, 20 mM KH203/K2H03 pH 6.8, 0.1 % LDAO 20 ul sitting drop, 10 protein : 10 precipitant Microcrystals: 8.5 mg/ml protein 18.5 ul sitting drop, 10 protein : 7.5 precipitant : 1 seed stock

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Data collection

DiffractionMean temperature: 293 K / Serial crystal experiment: Y
Diffraction sourceSource: FREE ELECTRON LASER / Site: SLAC LCLS / Beamline: CXI / Wavelength: 1.3 Å
DetectorType: CS-PAD CXI-1 / Detector: PIXEL / Date: Jun 13, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.3 Å / Relative weight: 1
ReflectionResolution: 2.8→35.8 Å / Num. obs: 75091 / % possible obs: 100 % / Redundancy: 5350 % / Biso Wilson estimate: 98.13 Å2 / CC1/2: 0.998 / Net I/σ(I): 16.42
Reflection shellResolution: 2.8→2.83 Å / Mean I/σ(I) obs: 2.33 / Num. unique obs: 4961 / CC1/2: 0.908
Serial crystallography sample deliveryMethod: injection

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
PHENIX1.17.1_3660refinement
CrystFEL0.6.3data reduction
CrystFEL0.6.3data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2I5N

2i5n


Resolution: 2.8→34.31 Å / SU ML: 0.2699 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.7647
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1832 3635 4.97 %
Rwork0.1594 69446 -
obs0.1606 73081 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 92.72 Å2
Refinement stepCycle: LAST / Resolution: 2.8→34.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9347 0 909 146 10402
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008311749
X-RAY DIFFRACTIONf_angle_d2.08916165
X-RAY DIFFRACTIONf_chiral_restr0.06341591
X-RAY DIFFRACTIONf_plane_restr0.01021982
X-RAY DIFFRACTIONf_dihedral_angle_d21.07824222
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8-2.840.28461390.27032648X-RAY DIFFRACTION99.89
2.84-2.880.30141380.26052621X-RAY DIFFRACTION99.86
2.88-2.920.26051270.24822647X-RAY DIFFRACTION99.86
2.92-2.960.32041290.23922624X-RAY DIFFRACTION99.89
2.96-3.010.27511480.23382628X-RAY DIFFRACTION99.75
3.01-3.060.26121150.24262668X-RAY DIFFRACTION99.78
3.06-3.110.25371460.21492604X-RAY DIFFRACTION99.96
3.11-3.160.24531270.20782676X-RAY DIFFRACTION100
3.16-3.230.23581410.2012629X-RAY DIFFRACTION100
3.23-3.290.2011170.17852664X-RAY DIFFRACTION100
3.29-3.360.19241500.16732635X-RAY DIFFRACTION100
3.36-3.440.20271350.16112661X-RAY DIFFRACTION100
3.44-3.530.16211400.15622644X-RAY DIFFRACTION100
3.53-3.620.19041430.15662637X-RAY DIFFRACTION100
3.62-3.730.18991520.15232652X-RAY DIFFRACTION100
3.73-3.850.18191380.14892659X-RAY DIFFRACTION100
3.85-3.990.16811210.14742679X-RAY DIFFRACTION99.96
3.99-4.150.16051580.1422657X-RAY DIFFRACTION100
4.15-4.330.16371350.14232669X-RAY DIFFRACTION99.96
4.33-4.560.17471540.14722684X-RAY DIFFRACTION100
4.56-4.850.19751550.14312656X-RAY DIFFRACTION100
4.85-5.220.16441460.14552695X-RAY DIFFRACTION100
5.22-5.740.18791310.15012725X-RAY DIFFRACTION100
5.74-6.570.20371340.14882736X-RAY DIFFRACTION100
6.57-8.260.1521510.13952765X-RAY DIFFRACTION99.97
8.26-34.310.16731650.17552883X-RAY DIFFRACTION99.93

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