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- PDB-6dho: RT XFEL structure of the two-flash state of Photosystem II (2F, S... -

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Entry
Database: PDB / ID: 6dho
TitleRT XFEL structure of the two-flash state of Photosystem II (2F, S3-rich) at 2.07 Angstrom resolution
Components
  • (Cytochrome b559 subunit ...) x 2
  • (Photosystem II ...) x 17
  • Cytochrome c-550
KeywordsPHOTOSYNTHESIS / PHOTOSYSTEMS / TRANSMEMBRANE / ROOM TEMPERATURE / ELECTRON TRANSPORT
Function / homology
Function and homology information


photosystem II assembly / photosystem II stabilization / oxygen evolving activity / photosystem II oxygen evolving complex / photosystem II / photosystem II reaction center / photosynthetic electron transport chain / oxidoreductase activity, acting on diphenols and related substances as donors, oxygen as acceptor / response to herbicide / photosystem II ...photosystem II assembly / photosystem II stabilization / oxygen evolving activity / photosystem II oxygen evolving complex / photosystem II / photosystem II reaction center / photosynthetic electron transport chain / oxidoreductase activity, acting on diphenols and related substances as donors, oxygen as acceptor / response to herbicide / photosystem II / extrinsic component of membrane / photosynthetic electron transport in photosystem II / chlorophyll binding / plasma membrane-derived thylakoid membrane / photosynthesis, light reaction / electron transporter, transferring electrons within the cyclic electron transport pathway of photosynthesis activity / phosphate ion binding / photosynthesis / respiratory electron transport chain / manganese ion binding / electron transfer activity / protein stabilization / iron ion binding / heme binding / metal ion binding
Similarity search - Function
Photosystem II protein Y (PsbY) / Photosystem II PsbY / Photosystem II PsbU, oxygen evolving complex / Photosystem II 12 kDa extrinsic protein (PsbU) / Photosystem II PsbV, cytochrome c-550 precursor / Photosystem II cytochrome c-550 precursor / Cytochrome c-550 domain / Cytochrome c-550 domain / Photosystem II PsbJ / Photosystem II PsbJ superfamily ...Photosystem II protein Y (PsbY) / Photosystem II PsbY / Photosystem II PsbU, oxygen evolving complex / Photosystem II 12 kDa extrinsic protein (PsbU) / Photosystem II PsbV, cytochrome c-550 precursor / Photosystem II cytochrome c-550 precursor / Cytochrome c-550 domain / Cytochrome c-550 domain / Photosystem II PsbJ / Photosystem II PsbJ superfamily / PsbJ / Photosystem II reaction centre protein Ycf12 / Photosystem II complex subunit Ycf12 / Photosystem II PsbX, type 1 subfamily / Photosystem II PsbO, manganese-stabilising / Manganese-stabilising protein / photosystem II polypeptide / Photosystem II reaction centre M protein (PsbM) / Photosystem II PsbM superfamily / Photosystem II PsbZ, reaction centre / Photosystem II PsbZ superfamily / YCF9 / Photosystem II PsbM / Photosystem II PsbX / Photosystem II reaction centre X protein (PsbX) / Photosystem II PsbT / Photosystem II PsbL / Photosystem II PsbL superfamily / Photosystem II PsbT superfamily / Photosystem II CP43 reaction centre protein superfamily / Photosystem II reaction centre T protein / PsbL protein / Photosystem II PsbK / Photosystem II CP43 reaction centre protein / Photosystem II PsbK superfamily / Photosystem II 4 kDa reaction centre component / Photosystem II CP47 reaction centre protein / Photosystem II PsbI / Photosystem II PsbI superfamily / Photosystem II reaction centre I protein (PSII 4.8 kDa protein) / Photosystem II reaction centre protein H / Photosystem II protein D1 / Photosystem II D2 protein / Photosystem II cytochrome b559, conserved site / Photosystem II cytochrome b559, alpha subunit / Photosystem II cytochrome b559, beta subunit / Photosystem II cytochrome b559, N-terminal / Photosystem II cytochrome b559, alpha subunit, lumenal region / Photosystem II reaction centre protein H superfamily / Photosystem II cytochrome b559, alpha subunit superfamily / Cytochrome b559, alpha (gene psbE) and beta (gene psbF)subunits / Lumenal portion of Cytochrome b559, alpha (gene psbE) subunit / Photosystem II 10 kDa phosphoprotein / Cytochrome b559 subunits heme-binding site signature. / Photosystem antenna protein-like / Photosystem antenna protein-like superfamily / Photosystem II protein / Outer membrane protein/outer membrane enzyme PagP, beta-barrel / Photosynthetic reaction centre, L/M / Photosystem II protein D1/D2 superfamily / Photosynthetic reaction centre protein / Photosynthetic reaction center proteins signature. / Cytochrome c family profile. / Cytochrome c-like domain / Cytochrome c-like domain superfamily
Similarity search - Domain/homology
BETA-CAROTENE / BICARBONATE ION / CHLOROPHYLL A / DIGALACTOSYL DIACYL GLYCEROL (DGDG) / : / HEME C / PROTOPORPHYRIN IX CONTAINING FE / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / CA-MN4-O5 CLUSTER ...BETA-CAROTENE / BICARBONATE ION / CHLOROPHYLL A / DIGALACTOSYL DIACYL GLYCEROL (DGDG) / : / HEME C / PROTOPORPHYRIN IX CONTAINING FE / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / CA-MN4-O5 CLUSTER / CA-MN4-O6 CLUSTER / PHEOPHYTIN A / Chem-PL9 / Chem-SQD / Unknown ligand / Photosystem II extrinsic protein V / Photosystem II extrinsic protein O / Photosystem II protein D1 1 / Photosystem II reaction center protein J / Photosystem II D2 protein / Photosystem II reaction center protein M / Photosystem II reaction center protein Z / Photosystem II CP43 reaction center protein / Photosystem II reaction center protein L / Cytochrome b559 subunit beta / Cytochrome b559 subunit alpha / Photosystem II reaction center protein T / Photosystem II CP47 reaction center protein / Photosystem II reaction center protein H / Photosystem II reaction center protein Psb30 / Photosystem II reaction center protein I / Photosystem II reaction center protein Y / Photosystem II reaction center protein K / Photosystem II extrinsic protein U / Photosystem II reaction center protein X
Similarity search - Component
Biological speciesThermosynechococcus elongatus (bacteria)
MethodX-RAY DIFFRACTION / FREE ELECTRON LASER / MOLECULAR REPLACEMENT / Resolution: 2.07 Å
AuthorsKern, J. / Chatterjee, R. / Young, I.D. / Fuller, F.D. / Lassalle, L. / Ibrahim, M. / Gul, S. / Fransson, T. / Brewster, A.S. / Alonso-Mori, R. ...Kern, J. / Chatterjee, R. / Young, I.D. / Fuller, F.D. / Lassalle, L. / Ibrahim, M. / Gul, S. / Fransson, T. / Brewster, A.S. / Alonso-Mori, R. / Hussein, R. / Zhang, M. / Douthit, L. / de Lichtenberg, C. / Cheah, M.H. / Shevela, D. / Wersig, J. / Seufert, I. / Sokaras, D. / Pastor, E. / Weninger, C. / Kroll, T. / Sierra, R.G. / Aller, P. / Butryn, A. / Orville, A.M. / Liang, M. / Batyuk, A. / Koglin, J.E. / Carbajo, S. / Boutet, S. / Moriarty, N.W. / Holton, J.M. / Dobbek, H. / Adams, P.D. / Bergmann, U. / Sauter, N.K. / Zouni, A. / Messinger, J. / Yano, J. / Yachandra, V.K.
Funding support United States, Germany, Sweden, United Kingdom, 21items
OrganizationGrant numberCountry
Department of Energy (DOE, United States)DE-AC02-05CH11231 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM055302 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM110501 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM126289 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM117126 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM116423-02 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM124149 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM124169 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)5 F32 GM116423-02 United States
Human Frontier Science Program (HFSP)RGP0063/2013 310 United States
German Research Foundation (DFG)Clusters of Excellence Unifying Concepts in Catalysis (UniCat) Germany
German Research Foundation (DFG)Sfb1078, TP A5 Germany
Other governmentUmea University, Solar Fuels Strong Research Environment Sweden
Knut and Alice Wallenberg Foundation2011.0055 Sweden
Swedish Research Council2016-05183 Sweden
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P41GM103393 United States
Department of Energy (DOE, United States)DE-AC02-76SF00515 United States
Biotechnology and Biological Sciences Research Council (BBSRC)102593 United Kingdom
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P41GM111244 United States
National Institutes of Health/Office of the DirectorS10OD021832 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P30 GM124169 United States
Citation
Journal: Nature / Year: 2018
Title: Structures of the intermediates of Kok's photosynthetic water oxidation clock.
Authors: Kern, J. / Chatterjee, R. / Young, I.D. / Fuller, F.D. / Lassalle, L. / Ibrahim, M. / Gul, S. / Fransson, T. / Brewster, A.S. / Alonso-Mori, R. / Hussein, R. / Zhang, M. / Douthit, L. / de ...Authors: Kern, J. / Chatterjee, R. / Young, I.D. / Fuller, F.D. / Lassalle, L. / Ibrahim, M. / Gul, S. / Fransson, T. / Brewster, A.S. / Alonso-Mori, R. / Hussein, R. / Zhang, M. / Douthit, L. / de Lichtenberg, C. / Cheah, M.H. / Shevela, D. / Wersig, J. / Seuffert, I. / Sokaras, D. / Pastor, E. / Weninger, C. / Kroll, T. / Sierra, R.G. / Aller, P. / Butryn, A. / Orville, A.M. / Liang, M. / Batyuk, A. / Koglin, J.E. / Carbajo, S. / Boutet, S. / Moriarty, N.W. / Holton, J.M. / Dobbek, H. / Adams, P.D. / Bergmann, U. / Sauter, N.K. / Zouni, A. / Messinger, J. / Yano, J. / Yachandra, V.K.
#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 Biol Crystallogr / Year: 2010
Title: PHENIX: a comprehensive Python-based system for macromolecular structure solution.
Authors: Paul D Adams / Pavel V Afonine / Gábor Bunkóczi / Vincent B Chen / Ian W Davis / Nathaniel Echols / Jeffrey J Headd / Li-Wei Hung / Gary J Kapral / Ralf W Grosse-Kunstleve / Airlie J McCoy ...Authors: Paul D Adams / Pavel V Afonine / Gábor Bunkóczi / Vincent B Chen / Ian W Davis / Nathaniel Echols / Jeffrey J Headd / Li-Wei Hung / Gary J Kapral / Ralf W Grosse-Kunstleve / Airlie J McCoy / Nigel W Moriarty / Robert Oeffner / Randy J Read / David C Richardson / Jane S Richardson / Thomas C Terwilliger / Peter H Zwart /
Abstract: Macromolecular X-ray crystallography is routinely applied to understand biological processes at a molecular level. However, significant time and effort are still required to solve and complete many ...Macromolecular X-ray crystallography is routinely applied to understand biological processes at a molecular level. However, significant time and effort are still required to solve and complete many of these structures because of the need for manual interpretation of complex numerical data using many software packages and the repeated use of interactive three-dimensional graphics. PHENIX has been developed to provide a comprehensive system for macromolecular crystallographic structure solution with an emphasis on the automation of all procedures. This has relied on the development of algorithms that minimize or eliminate subjective input, the development of algorithms that automate procedures that are traditionally performed by hand and, finally, the development of a framework that allows a tight integration between the algorithms.
#3: Journal: Acta Crystallogr D Struct Biol / Year: 2018
Title: DIALS: implementation and evaluation of a new integration package.
Authors: Winter, G. / Waterman, D.G. / Parkhurst, J.M. / Brewster, A.S. / Gildea, R.J. / Gerstel, M. / Fuentes-Montero, L. / Vollmar, M. / Michels-Clark, T. / Young, I.D. / Sauter, N.K. / Evans, G.
#4: Journal: Acta Crystallogr D Biol Crystallogr / Year: 2010
Title: Features and development of Coot.
Authors: P Emsley / B Lohkamp / W G Scott / K Cowtan /
Abstract: Coot is a molecular-graphics application for model building and validation of biological macromolecules. The program displays electron-density maps and atomic models and allows model manipulations ...Coot is a molecular-graphics application for model building and validation of biological macromolecules. The program displays electron-density maps and atomic models and allows model manipulations such as idealization, real-space refinement, manual rotation/translation, rigid-body fitting, ligand search, solvation, mutations, rotamers and Ramachandran idealization. Furthermore, tools are provided for model validation as well as interfaces to external programs for refinement, validation and graphics. The software is designed to be easy to learn for novice users, which is achieved by ensuring that tools for common tasks are 'discoverable' through familiar user-interface elements (menus and toolbars) or by intuitive behaviour (mouse controls). Recent developments have focused on providing tools for expert users, with customisable key bindings, extensions and an extensive scripting interface. The software is under rapid development, but has already achieved very widespread use within the crystallographic community. The current state of the software is presented, with a description of the facilities available and of some of the underlying methods employed.
#5: Journal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2014
Title: Protein structural ensembles are revealed by redefining X-ray electron density noise.
Authors: Lang, P.T. / Holton, J.M. / Fraser, J.S. / Alber, T.
History
DepositionMay 20, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 21, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 28, 2018Group: Data collection / Database references
Category: citation / diffrn_radiation_wavelength / diffrn_source
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _diffrn_radiation_wavelength.wavelength / _diffrn_source.pdbx_synchrotron_beamline / _diffrn_source.pdbx_synchrotron_site
Revision 1.2Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support
Item: _pdbx_audit_support.funding_organization / _pdbx_audit_support.grant_number
Revision 1.3Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 2.0Mar 10, 2021Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / diffrn_radiation_wavelength / entity / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_close_contact / struct_asym / struct_conn / struct_conn_type / struct_site
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.auth_comp_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _diffrn_radiation_wavelength.wavelength / _pdbx_nonpoly_scheme.entity_id / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.pdb_mon_id / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_alt_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _pdbx_unobs_or_zero_occ_atoms.auth_atom_id / _pdbx_unobs_or_zero_occ_atoms.label_atom_id / _pdbx_validate_close_contact.auth_comp_id_2 / _struct_asym.entity_id / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id / _struct_site.details / _struct_site.pdbx_auth_comp_id
Revision 3.0Oct 11, 2023Group: Data collection / Database references ...Data collection / Database references / Non-polymer description / Refinement description
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_validate_chiral
Item: _chem_comp.formula / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 3.1Mar 13, 2024Group: Source and taxonomy / Structure summary / Category: entity / entity_src_nat / Item: _entity.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Photosystem II protein D1 1
B: Photosystem II CP47 reaction center protein
C: Photosystem II CP43 reaction center protein
D: Photosystem II D2 protein
E: Cytochrome b559 subunit alpha
F: Cytochrome b559 subunit beta
H: Photosystem II reaction center protein H
I: Photosystem II reaction center protein I
J: Photosystem II reaction center protein J
K: Photosystem II reaction center protein K
L: Photosystem II reaction center protein L
M: Photosystem II reaction center protein M
O: Photosystem II manganese-stabilizing polypeptide
T: Photosystem II reaction center protein T
U: Photosystem II 12 kDa extrinsic protein
V: Cytochrome c-550
Y: Photosystem II reaction center protein Ycf12
X: Photosystem II reaction center X protein
Z: Photosystem II reaction center protein Z
R: Photosystem II protein Y
a: Photosystem II protein D1 1
b: Photosystem II CP47 reaction center protein
c: Photosystem II CP43 reaction center protein
d: Photosystem II D2 protein
e: Cytochrome b559 subunit alpha
f: Cytochrome b559 subunit beta
h: Photosystem II reaction center protein H
i: Photosystem II reaction center protein I
j: Photosystem II reaction center protein J
k: Photosystem II reaction center protein K
l: Photosystem II reaction center protein L
m: Photosystem II reaction center protein M
o: Photosystem II manganese-stabilizing polypeptide
t: Photosystem II reaction center protein T
u: Photosystem II 12 kDa extrinsic protein
v: Cytochrome c-550
y: Photosystem II reaction center protein Ycf12
x: Photosystem II reaction center X protein
z: Photosystem II reaction center protein Z
r: Photosystem II protein Y
hetero molecules


Theoretical massNumber of molelcules
Total (without water)720,029228
Polymers590,60840
Non-polymers129,421188
Water36,5882031
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)117.011, 221.542, 308.346
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
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

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Photosystem II ... , 17 types, 34 molecules AaBbCcDdHhIiJjKkLlMmOoTtUuYyXx...

#1: Protein Photosystem II protein D1 1 / / PSII D1 protein 1 / Photosystem II Q(B) protein 1


Mass: 37059.258 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: cell
Source: (natural) Thermosynechococcus elongatus (strain BP-1) (bacteria)
Strain: BP-1 / References: UniProt: P0A444, photosystem II
#2: Protein Photosystem II CP47 reaction center protein / / PSII 47 kDa protein / Protein CP-47


Mass: 56096.758 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: cell
Source: (natural) Thermosynechococcus elongatus (strain BP-1) (bacteria)
Strain: BP-1 / References: UniProt: Q8DIQ1
#3: Protein Photosystem II CP43 reaction center protein / / PSII 43 kDa protein / Protein CP-43


Mass: 49207.250 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: cell
Source: (natural) Thermosynechococcus elongatus (strain BP-1) (bacteria)
Strain: BP-1 / References: UniProt: Q8DIF8
#4: Protein Photosystem II D2 protein / / PSII D2 protein / Photosystem II Q(A) protein


Mass: 38275.836 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: cell
Source: (natural) Thermosynechococcus elongatus (strain BP-1) (bacteria)
Strain: BP-1 / References: UniProt: Q8CM25, photosystem II
#7: Protein Photosystem II reaction center protein H / / PSII-H


Mass: 7227.559 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: cell
Source: (natural) Thermosynechococcus elongatus (strain BP-1) (bacteria)
Strain: BP-1 / References: UniProt: Q8DJ43
#8: Protein/peptide Photosystem II reaction center protein I / / PSII-I / PSII 4.4 kDa protein


Mass: 4195.983 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: cell / Source: (natural) Thermosynechococcus elongatus (bacteria) / Strain: BP-1 / References: UniProt: Q8DJZ6
#9: Protein/peptide Photosystem II reaction center protein J / / PSII-J


Mass: 3627.325 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: cell
Source: (natural) Thermosynechococcus elongatus (strain BP-1) (bacteria)
Strain: BP-1 / References: UniProt: P59087
#10: Protein/peptide Photosystem II reaction center protein K / / PSII-K


Mass: 4101.911 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: cell
Source: (natural) Thermosynechococcus elongatus (strain BP-1) (bacteria)
Strain: BP-1 / References: UniProt: Q9F1K9
#11: Protein/peptide Photosystem II reaction center protein L / / PSII-L


Mass: 4299.044 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: cell
Source: (natural) Thermosynechococcus elongatus (strain BP-1) (bacteria)
Strain: BP-1 / References: UniProt: Q8DIN8
#12: Protein/peptide Photosystem II reaction center protein M / / PSII-M


Mass: 3706.348 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: cell / Source: (natural) Thermosynechococcus elongatus (bacteria) / Strain: BP-1 / References: UniProt: Q8DHA7
#13: Protein Photosystem II manganese-stabilizing polypeptide / / MSP


Mass: 26651.707 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: cell
Source: (natural) Thermosynechococcus elongatus (strain BP-1) (bacteria)
Strain: BP-1 / References: UniProt: P0A431
#14: Protein/peptide Photosystem II reaction center protein T / / PSII-Tc


Mass: 3648.379 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: cell / Source: (natural) Thermosynechococcus elongatus (bacteria) / Strain: BP-1 / References: UniProt: Q8DIQ0
#15: Protein Photosystem II 12 kDa extrinsic protein / / PS II complex 12 kDa extrinsic protein / PSII-U


Mass: 10966.317 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: cell
Source: (natural) Thermosynechococcus elongatus (strain BP-1) (bacteria)
Strain: BP-1 / References: UniProt: Q9F1L5
#17: Protein/peptide Photosystem II reaction center protein Ycf12 /


Mass: 3228.035 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: cell
Source: (natural) Thermosynechococcus elongatus (strain BP-1) (bacteria)
Strain: BP-1 / References: UniProt: Q8DJI1
#18: Protein/peptide Photosystem II reaction center X protein /


Mass: 3990.795 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: cell
Source: (natural) Thermosynechococcus elongatus (strain BP-1) (bacteria)
Strain: BP-1 / References: UniProt: Q9F1R6
#19: Protein Photosystem II reaction center protein Z / / PSII-Z


Mass: 6766.187 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: cell
Source: (natural) Thermosynechococcus elongatus (strain BP-1) (bacteria)
Strain: BP-1 / References: UniProt: Q8DHJ2
#20: Protein/peptide Photosystem II protein Y /


Mass: 3859.732 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: cell
Source: (natural) Thermosynechococcus elongatus (strain BP-1) (bacteria)
Strain: BP-1 / References: UniProt: Q8DKM3

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Cytochrome b559 subunit ... , 2 types, 4 molecules EeFf

#5: Protein Cytochrome b559 subunit alpha / / PSII reaction center subunit V


Mass: 9378.566 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: cell
Source: (natural) Thermosynechococcus elongatus (strain BP-1) (bacteria)
Strain: BP-1 / References: UniProt: Q8DIP0
#6: Protein/peptide Cytochrome b559 subunit beta / / PSII reaction center subunit VI


Mass: 3868.611 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: cell
Source: (natural) Thermosynechococcus elongatus (strain BP-1) (bacteria)
Strain: BP-1 / References: UniProt: Q8DIN9

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Protein / Sugars , 2 types, 12 molecules Vv

#16: Protein Cytochrome c-550 / Cytochrome c-549 / Cytochrome c550 / Low-potential cytochrome c


Mass: 15148.255 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: cell
Source: (natural) Thermosynechococcus elongatus (strain BP-1) (bacteria)
Strain: BP-1 / References: UniProt: P0A386
#30: Sugar
ChemComp-DGD / DIGALACTOSYL DIACYL GLYCEROL (DGDG)


Type: saccharideCarbohydrate / Mass: 949.299 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C51H96O15

-
Non-polymers , 16 types, 2209 molecules

#21: Chemical ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: Fe / Details: cell
#22: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#23: Chemical...
ChemComp-CLA / CHLOROPHYLL A / PSII-Z / Chlorophyll a


Mass: 893.489 Da / Num. of mol.: 70 / Source method: isolated from a natural source / Formula: C55H72MgN4O5 / Details: cell
#24: Chemical
ChemComp-PHO / PHEOPHYTIN A / Pheophytin


Mass: 871.200 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C55H74N4O5
#25: Chemical...
ChemComp-BCR / BETA-CAROTENE / Β-Carotene


Mass: 536.873 Da / Num. of mol.: 22 / Source method: obtained synthetically / Formula: C40H56
#26: Chemical
ChemComp-PL9 / 2,3-DIMETHYL-5-(3,7,11,15,19,23,27,31,35-NONAMETHYL-2,6,10,14,18,22,26,30,34-HEXATRIACONTANONAENYL-2,5-CYCLOHEXADIENE-1,4-DIONE-2,3-DIMETHYL-5-SOLANESYL-1,4-BENZOQUINONE / PLASTOQUINONE 9 / Plastoquinone


Mass: 749.201 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C53H80O2
#27: Chemical
ChemComp-LMG / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE


Mass: 787.158 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: C45H86O10
#28: Chemical
ChemComp-SQD / 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL / SULFOQUINOVOSYLDIACYLGLYCEROL


Mass: 795.116 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C41H78O12S
#29: Chemical
ChemComp-LHG / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / Phosphatidylglycerol


Mass: 722.970 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C38H75O10P / Comment: phospholipid*YM
#31: Chemical ChemComp-OEX / CA-MN4-O5 CLUSTER


Mass: 339.827 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CaMn4O5
#32: Chemical ChemComp-OEY / CA-MN4-O6 CLUSTER


Mass: 355.827 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CaMn4O6
#33: Chemical ChemComp-BCT / BICARBONATE ION / Bicarbonate


Mass: 61.017 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CHO3 / Comment: pH buffer*YM
#34: Chemical...
ChemComp-UNL / UNKNOWN LIGAND


Mass: 355.827 Da / Num. of mol.: 31 / Source method: obtained synthetically
#35: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#36: Chemical ChemComp-HEC / HEME C / Heme C


Mass: 618.503 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H34FeN4O4
#37: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 2031 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 3.4 Å3/Da / Density % sol: 63.8 % / Description: Cube-like crystals
Crystal growTemperature: 298 K / Method: batch mode / pH: 6.5 / Details: 0.1 M MES pH 6.5, 0.1 M NH4Cl, 35% (w/v) PEG 5000

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Data collection

Diffraction
IDMean temperature (K)Crystal-IDSerial crystal experiment
12981Y
32981Y
22981Y
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
FREE ELECTRON LASERSLAC LCLS MFX11.305
FREE ELECTRON LASERSLAC LCLS MFX31.305
FREE ELECTRON LASERSLAC LCLS MFX21.305
Detector
TypeIDDetectorDateDetails
RAYONIX MX170-HS1CCDJul 14, 2016Compound refractive lenses
RAYONIX MX170-HS3CCDJul 13, 2017Compound refractive lenses
RAYONIX MX170-HS2CCDOct 20, 2016Compound refractive lenses
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1noneSINGLE WAVELENGTHMx-ray1
3noneSINGLE WAVELENGTHMx-ray2
2noneSINGLE WAVELENGTHMx-ray3
Radiation wavelength
IDWavelength (Å)Relative weight
11.3051
21
31
ReflectionResolution: 2.07→30.58 Å / Num. obs: 483509 / % possible obs: 99.96 % / Redundancy: 207.28 % / CC1/2: 0.982 / Net I/σ(I): 15.463
Reflection shell
Resolution (Å)Redundancy (%)Mean I/σ(I) obsCC1/2Diffraction-ID% possible all
5.619-30.58750.75122.8040.987199.23
4.46-5.619523.4563.1510.9791100
3.896-4.46461.2142.4370.9731100
3.54-3.896425.3423.2260.9581100
3.286-3.54398.114.8470.9361100
3.092-3.286363.848.7730.8861100
2.937-3.092300.595.5530.8111100
2.809-2.937192.174.0220.7271100
2.701-2.809135.53.140.6081100
2.608-2.701103.952.5480.4711100
2.526-2.60883.762.1630.3711100
2.454-2.52670.981.9540.271100
2.39-2.45459.711.6490.1941100
2.331-2.39521.5330.1191100
2.278-2.33145.51.3630.0941100
2.23-2.27839.751.2470.0661100
2.185-2.2334.551.1250.0371100
2.144-2.18528.330.9330.0411100
2.106-2.14420.810.7510.0251100
2.07-2.10613.750.5820.021199.98
Serial crystallography measurementFocal spot size: 3 µm2 / Pulse duration: 40 fsec. / Pulse energy: 3.63 µJ / Pulse photon energy: 9.515 keV / XFEL pulse repetition rate: 10 Hz
Serial crystallography sample deliveryMethod: fixed target

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Processing

Software
NameVersionClassification
PHENIXdev_svnrefinement
PDB_EXTRACT3.24data extraction
cctbx.xfeldata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5KAF

5kaf


Resolution: 2.07→30.578 Å / SU ML: 0.37 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 28.77
RfactorNum. reflection% reflection
Rfree0.2475 4285 0.89 %
Rwork0.1844 --
obs0.185 482673 99.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 181.33 Å2 / Biso mean: 46.7274 Å2 / Biso min: 12.98 Å2
Refinement stepCycle: final / Resolution: 2.07→30.578 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms41576 0 19205 1886 62667
Biso mean--50.1 43.02 -
Num. residues----5306
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.07-2.09350.42751360.3644155091564598
2.0935-2.11810.36241410.353156981583999
2.1181-2.1440.39231430.3411581915962100
2.144-2.17110.37151420.33031589616038100
2.1711-2.19970.37231440.32051583615980100
2.1997-2.22980.36141420.31061584215984100
2.2298-2.26160.36661390.30011588616025100
2.2616-2.29540.35571440.29191587816022100
2.2954-2.33120.31781420.28431584115983100
2.3312-2.36940.30951420.27451588316025100
2.3694-2.41030.361440.26761593016074100
2.4103-2.45410.31771420.25961586516007100
2.4541-2.50130.33861440.24731591916063100
2.5013-2.55230.28241430.23481587516018100
2.5523-2.60780.30011400.22941593416074100
2.6078-2.66840.28791440.2191592716071100
2.6684-2.73510.28661410.21291591416055100
2.7351-2.8090.29791430.20251588516028100
2.809-2.89160.27491420.19851593916081100
2.8916-2.98480.27091440.1921598916133100
2.9848-3.09140.23361420.18191596516107100
3.0914-3.21510.26041440.17951598016124100
3.2151-3.36120.22981430.15941601216155100
3.3612-3.53820.22951440.15371601816162100
3.5382-3.75950.19731430.14231602916172100
3.7595-4.04920.18361450.13341604216187100
4.0492-4.45550.18161440.12321604916193100
4.4555-5.09770.18091440.12131614716291100
5.0977-6.41280.22231450.14421623516380100
6.4128-30.58180.20571490.1422166461679599

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