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- PDB-4tnh: RT XFEL structure of Photosystem II in the dark state at 4.9 A re... -

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Basic information

Entry
Database: PDB / ID: 4tnh
TitleRT XFEL structure of Photosystem II in the dark state at 4.9 A resolution
Components
  • (Cytochrome b559 subunit ...) x 2
  • (Photosystem II ...) x 16
  • Cytochrome c-550
  • Photosystem Q(B) protein 1
KeywordsELECTRON TRANSPORT / PHOTOSYNTHESIS / water oxidation / membrane protein / X-ray free electron laser
Function / homology
Function and homology information


photosystem II oxygen evolving complex / photosystem II assembly / oxygen evolving activity / photosystem II stabilization / photosystem II reaction center / photosystem II / oxidoreductase activity, acting on diphenols and related substances as donors, oxygen as acceptor / photosynthetic electron transport chain / response to herbicide / extrinsic component of membrane ...photosystem II oxygen evolving complex / photosystem II assembly / oxygen evolving activity / photosystem II stabilization / photosystem II reaction center / photosystem II / oxidoreductase activity, acting on diphenols and related substances as donors, oxygen as acceptor / photosynthetic electron transport chain / response to herbicide / extrinsic component of membrane / photosystem II / photosynthesis, light reaction / phosphate ion binding / photosynthetic electron transport in photosystem II / chlorophyll binding / plasma membrane-derived thylakoid membrane / electron transporter, transferring electrons within the cyclic electron transport pathway of photosynthesis activity / photosynthesis / respiratory electron transport chain / electron transfer activity / protein stabilization / iron ion binding / heme binding / metal ion binding
Similarity search - Function
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 PsbO, manganese-stabilising ...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 PsbO, manganese-stabilising / Manganese-stabilising protein / photosystem II polypeptide / Photosystem II reaction centre protein Ycf12 / Photosystem II complex subunit Ycf12 / Photosystem II PsbX, type 1 subfamily / Photosystem II reaction centre M protein (PsbM) / Photosystem II PsbM superfamily / Photosystem II PsbM / Photosystem II PsbZ, reaction centre / Photosystem II PsbZ superfamily / YCF9 / 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 reaction centre T protein / PsbL protein / Photosystem II CP43 reaction centre protein / Photosystem II CP43 reaction centre protein superfamily / Photosystem II PsbK / 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 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 / Photosystem II protein D1 / 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) / : / PROTOPORPHYRIN IX CONTAINING FE / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / CA-MN4-O5 CLUSTER / PHEOPHYTIN A ...BETA-CAROTENE / BICARBONATE ION / CHLOROPHYLL A / DIGALACTOSYL DIACYL GLYCEROL (DGDG) / : / PROTOPORPHYRIN IX CONTAINING FE / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / CA-MN4-O5 CLUSTER / PHEOPHYTIN A / Chem-PL9 / Chem-SQD / 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 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: 4.90000680874 Å
AuthorsKern, J. / Tran, R. / Alonso-Mori, R. / Koroidov, S. / Echols, N. / Hattne, J. / Ibrahim, M. / Gul, S. / Laksmono, H. / Sierra, R.G. ...Kern, J. / Tran, R. / Alonso-Mori, R. / Koroidov, S. / Echols, N. / Hattne, J. / Ibrahim, M. / Gul, S. / Laksmono, H. / Sierra, R.G. / Gildea, R.J. / Han, G. / Hellmich, J. / Lassalle-Kaiser, B. / Chatterjee, R. / Brewster, A. / Stan, C.A. / Gloeckner, C. / Lampe, A. / DiFiore, D. / Milathianaki, D. / Fry, A.R. / Seibert, M.M. / Koglin, J.E. / Gallo, E. / Uhlig, J. / Sokaras, D. / Weng, T.-C. / Zwart, P.H. / Skinner, D.E. / Bogan, M.J. / Messerschmidt, M. / Glatzel, P. / Williams, G.J. / Boutet, S. / Adams, P.D. / Zouni, A. / Messinger, J. / Sauter, N.K. / Bergmann, U. / Yano, J. / Yachandra, V.K.
Funding support United States, 5items
OrganizationGrant numberCountry
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)P41GM103393 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM095887 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM102520 United States
Department of Energy (DOE, United States)DE-AC02-05CH11231 United States
Citation
Journal: Nat Commun / Year: 2014
Title: Taking snapshots of photosynthetic water oxidation using femtosecond X-ray diffraction and spectroscopy.
Authors: Kern, J. / Tran, R. / Alonso-Mori, R. / Koroidov, S. / Echols, N. / Hattne, J. / Ibrahim, M. / Gul, S. / Laksmono, H. / Sierra, R.G. / Gildea, R.J. / Han, G. / Hellmich, J. / Lassalle- ...Authors: Kern, J. / Tran, R. / Alonso-Mori, R. / Koroidov, S. / Echols, N. / Hattne, J. / Ibrahim, M. / Gul, S. / Laksmono, H. / Sierra, R.G. / Gildea, R.J. / Han, G. / Hellmich, J. / Lassalle-Kaiser, B. / Chatterjee, R. / Brewster, A.S. / Stan, C.A. / Glockner, C. / Lampe, A. / DiFiore, D. / Milathianaki, D. / Fry, A.R. / Seibert, M.M. / Koglin, J.E. / Gallo, E. / Uhlig, J. / Sokaras, D. / Weng, T.C. / Zwart, P.H. / Skinner, D.E. / Bogan, M.J. / Messerschmidt, M. / Glatzel, P. / Williams, G.J. / Boutet, S. / Adams, P.D. / Zouni, A. / Messinger, J. / Sauter, N.K. / Bergmann, U. / 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.
History
DepositionJun 4, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 9, 2014Provider: repository / Type: Initial release
Revision 1.1Jul 23, 2014Group: Database references
Revision 1.2Oct 7, 2015Group: Other
Revision 1.3Sep 27, 2017Group: Author supporting evidence / Derived calculations / Refinement description
Category: pdbx_audit_support / pdbx_struct_oper_list / software
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation / _software.classification
Revision 1.4Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 2.0Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / 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 / struct_conn / struct_conn_type / struct_ncs_dom_lim
Item: _chem_comp.formula / _database_2.pdbx_DOI ..._chem_comp.formula / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_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 2.1Oct 23, 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: Photosystem Q(B) protein 1
B: Photosystem II core light harvesting protein
C: Photosystem II CP43 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
Y: Photosystem II reaction center protein Y
Z: Photosystem II reaction center protein Z
a: Photosystem Q(B) protein 1
b: Photosystem II core light harvesting protein
c: Photosystem II CP43 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
g: Photosystem II reaction center protein Ycf12
x: Photosystem II reaction center X protein
G: Photosystem II reaction center protein Y
z: Photosystem II reaction center protein Z
hetero molecules


Theoretical massNumber of molelcules
Total (without water)762,725224
Polymers627,10640
Non-polymers135,619184
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)132.885, 229.033, 307.715
Angle α, β, γ (deg.)90.0, 90.0, 90.0
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
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
12
22
13
23
14
24
15
25
16
26
17
27
18
28
19
29
110
210
111
211
112
212
113
213
114
214
115
215
116
216
117
217
118
218
119
219

NCS domain segments:

Component-ID: 1

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11SERSERALAALAchain 'A'AA10 - 34410 - 344
21SERSERALAALAchain 'a'aU10 - 34410 - 344
12GLYGLYVALVALchain 'B'BB2 - 4912 - 491
22GLYGLYVALVALchain 'b'bV2 - 4912 - 491
13ASPASPASPASPchain 'C'CC27 - 47315 - 461
23ASPASPASPASPchain 'c'cW27 - 47315 - 461
14GLYGLYLEULEUchain 'D'DD13 - 35213 - 352
24GLYGLYLEULEUchain 'd'dX13 - 35213 - 352
15GLYGLYLYSLYSchain 'E'EE3 - 843 - 84
25GLYGLYLYSLYSchain 'e'eY3 - 843 - 84
16VALVALARGARGchain 'F'FF11 - 4511 - 45
26VALVALARGARGchain 'f'fZ11 - 4511 - 45
17ALAALAGLYGLYchain 'H'HG2 - 662 - 66
27ALAALAGLYGLYchain 'h'hAA2 - 662 - 66
18METMETLYSLYSchain 'I'IH1 - 351 - 35
28METMETLYSLYSchain 'i'iBA1 - 351 - 35
19ARGARGLEULEUchain 'J'JI7 - 407 - 40
29ARGARGLEULEUchain 'j'jCA7 - 407 - 40
110LYSLYSARGARGchain 'K'KJ10 - 4610 - 46
210LYSLYSARGARGchain 'k'kDA10 - 4610 - 46
111METMETASNASNchain 'L'LK1 - 371 - 37
211METMETASNASNchain 'l'lEA1 - 371 - 37
112METMETLYSLYSchain 'M'ML1 - 341 - 34
212METMETLYSLYSchain 'm'mFA1 - 341 - 34
113THRTHRALAALAchain 'O'OM30 - 27230 - 272
213THRTHRALAALAchain 'o'oGA30 - 27230 - 272
114METMETLYSLYSchain 'T'TN1 - 321 - 32
214METMETLYSLYSchain 't'tHA1 - 321 - 32
115GLUGLULYSLYSchain 'U'UO38 - 13438 - 134
215GLUGLULYSLYSchain 'u'uIA38 - 13438 - 134
116ALAALATYRTYRchain 'V'VP27 - 16327 - 163
216ALAALATYRTYRchain 'v'vJA27 - 16327 - 163
117THRTHRGLNGLNchain 'X'XR11 - 472 - 38
217THRTHRGLNGLNchain 'x'xLA11 - 472 - 38
118METMETVALVALchain 'Z'ZT1 - 621 - 62
218METMETVALVALchain 'z'zNA1 - 621 - 62
119ILEILELEULEUchain 'g'gKA19 - 4619 - 46
219ILEILELEULEUchain 'y'yQ19 - 4619 - 46

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19

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Components

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Protein , 2 types, 4 molecules AaVv

#1: Protein Photosystem Q(B) protein 1 / 32 kDa thylakoid membrane protein 1 / Photosystem II protein D1 1


Mass: 38265.625 Da / Num. of mol.: 2 / Fragment: UNP residues 1-344 / Source method: isolated from a natural source / Source: (natural) Thermosynechococcus elongatus (bacteria) / Strain: BP-1 / References: UniProt: P0A444, photosystem II
#16: Protein Cytochrome c-550 / Cytochrome c-549 / Cytochrome c550 / Low-potential cytochrome c


Mass: 18046.943 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermosynechococcus elongatus (bacteria) / Strain: BP-1 / References: UniProt: P0A386

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Photosystem II ... , 16 types, 32 molecules BbCcDdHhIiJjKkLlMmOoTtUuygXxYGZz

#2: Protein Photosystem II core light harvesting protein


Mass: 56656.457 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermosynechococcus elongatus (bacteria) / Strain: BP-1 / References: UniProt: Q8DIQ1
#3: Protein Photosystem II CP43 protein


Mass: 50287.500 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermosynechococcus elongatus (bacteria) / Strain: BP-1 / References: UniProt: Q8DIF8
#4: Protein Photosystem II D2 protein / PSII D2 protein / Photosystem Q(A) protein


Mass: 39388.156 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermosynechococcus elongatus (bacteria) / Strain: BP-1 / References: UniProt: Q8CM25, photosystem II
#7: Protein Photosystem II reaction center protein H / PSII-H


Mass: 7358.754 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermosynechococcus elongatus (bacteria) / Strain: BP-1 / References: UniProt: Q8DJ43
#8: Protein/peptide Photosystem II reaction center protein I / PSII-I / PSII 4.4 kDa protein


Mass: 4410.245 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermosynechococcus elongatus (bacteria) / Strain: BP-1 / References: UniProt: Q8DJZ6
#9: Protein/peptide Photosystem II reaction center protein J / PSII-J


Mass: 4105.908 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermosynechococcus elongatus (bacteria) / Strain: BP-1 / References: UniProt: P59087
#10: Protein/peptide Photosystem II reaction center protein K / PSII-K


Mass: 5028.083 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermosynechococcus elongatus (bacteria) / Strain: BP-1 / References: UniProt: Q9F1K9
#11: Protein/peptide Photosystem II reaction center protein L / PSII-L / PSII 5 kDa protein


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


Mass: 3981.673 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermosynechococcus elongatus (bacteria) / Strain: BP-1 / References: UniProt: Q8DHA7
#13: Protein Photosystem II manganese-stabilizing polypeptide / MSP


Mass: 29637.443 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermosynechococcus elongatus (bacteria) / Strain: BP-1 / References: UniProt: P0A431
#14: Protein/peptide Photosystem II reaction center protein T / PSII-Tc


Mass: 3878.728 Da / Num. of mol.: 2 / Source method: isolated from a natural source / 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: 15030.986 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermosynechococcus elongatus (bacteria) / Strain: BP-1 / References: UniProt: Q9F1L5
#17: Protein/peptide Photosystem II reaction center protein Ycf12


Mass: 5039.143 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermosynechococcus elongatus (bacteria) / Strain: BP-1 / References: UniProt: Q8DJI1
#18: Protein/peptide Photosystem II reaction center X protein


Mass: 4322.226 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermosynechococcus elongatus (bacteria) / Strain: BP-1 / References: UniProt: Q9F1R6
#19: Protein/peptide Photosystem II reaction center protein Y


Mass: 2400.951 Da / Num. of mol.: 2 / Fragment: See REMARK 999 / Source method: isolated from a natural source / Source: (natural) Thermosynechococcus elongatus (bacteria) / Strain: BP-1
#20: Protein Photosystem II reaction center protein Z / PSII-Z


Mass: 6766.187 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermosynechococcus elongatus (bacteria) / Strain: BP-1 / References: UniProt: Q8DHJ2

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

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


Mass: 9580.840 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermosynechococcus elongatus (bacteria) / Strain: BP-1 / References: UniProt: Q8DIP0
#6: Protein/peptide Cytochrome b559 subunit beta / PSII reaction center subunit VI


Mass: 5067.900 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermosynechococcus elongatus (bacteria) / Strain: BP-1 / References: UniProt: Q8DIN9

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Sugars , 2 types, 28 molecules

#25: Sugar
ChemComp-DGD / DIGALACTOSYL DIACYL GLYCEROL (DGDG)


Type: saccharide / Mass: 949.299 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C51H96O15
#31: Sugar
ChemComp-LMT / DODECYL-BETA-D-MALTOSIDE


Type: D-saccharide / Mass: 510.615 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C24H46O11 / Comment: detergent*YM

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Non-polymers , 13 types, 156 molecules

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


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe
#22: Chemical...
ChemComp-CLA / CHLOROPHYLL A


Mass: 893.489 Da / Num. of mol.: 70 / Source method: obtained synthetically / Formula: C55H72MgN4O5
#23: 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


Mass: 749.201 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C53H80O2
#24: Chemical...
ChemComp-BCR / BETA-CAROTENE


Mass: 536.873 Da / Num. of mol.: 24 / Source method: obtained synthetically / Formula: C40H56
#26: Chemical
ChemComp-LHG / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE


Mass: 722.970 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C38H75O10P / Comment: phospholipid*YM
#27: Chemical...
ChemComp-LMG / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE


Mass: 787.158 Da / Num. of mol.: 22 / Source method: obtained synthetically / Formula: C45H86O10
#28: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#29: Chemical ChemComp-OEX / CA-MN4-O5 CLUSTER


Mass: 339.827 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CaMn4O5
#30: 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.: 10 / Source method: obtained synthetically / Formula: C41H78O12S
#32: Chemical
ChemComp-PHO / PHEOPHYTIN A


Mass: 871.200 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C55H74N4O5
#33: Chemical ChemComp-BCT / BICARBONATE ION


Mass: 61.017 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CHO3 / Comment: pH buffer*YM
#34: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#35: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca

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Details

Has protein modificationY
Sequence detailsMolecule 19 (PHOTOSYSTEM II PROTEIN Y): THE DEPOSITORS STATE THAT THE SAMPLE SEQUENCE IS ...Molecule 19 (PHOTOSYSTEM II PROTEIN Y): THE DEPOSITORS STATE THAT THE SAMPLE SEQUENCE IS MDWRVLVVLLPVLLAAGWAVRNILPYAVKQVQKLLQKAKAA (UNP Q8DKM3).

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 6695

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Sample preparation

CrystalDensity Matthews: 3.66 Å3/Da / Density % sol: 66.36 %
Crystal growTemperature: 298 K / Method: batch mode / pH: 7
Details: 4% PEG2000, 5 mM calcium chloride, 100 mM PIPES, pH 7.0, BATCH, temperature 298K

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: FREE ELECTRON LASER / Site: SLAC LCLS / Beamline: CXI / Wavelength: 1.77 Å
DetectorType: CS-PAD detector / Detector: PIXEL / Date: Mar 3, 2013 / Details: KB mirrors
RadiationMonochromator: No monochromator, FEL beam with 20-30 eV bandwidth
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.77 Å / Relative weight: 1
ReflectionResolution: 4.9→72.93 Å / Num. obs: 41292 / % possible obs: 99.7 % / Redundancy: 65.4 % / Biso Wilson estimate: 171.542951793 Å2 / Net I/σ(I): 40.7
Reflection shellResolution: 4.9→5.08 Å / Redundancy: 7.6 % / Mean I/σ(I) obs: 3.9 / % possible all: 98.6

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: dev_1635+SVN)refinement
cctbx.xfeldata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3bz1

3bz1
PDB Unreleased entry


Resolution: 4.90000680874→72.9250039452 Å / SU ML: 0.743228973461 / Cross valid method: FREE R-VALUE / σ(F): 1.38126417 / Phase error: 30.4494599668
RfactorNum. reflection% reflection
Rfree0.291771032118 3986 4.8966254315 %
Rwork0.280546821323 77417 -
obs0.281090212356 81403 97.7074406155 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 206.869966682 Å2
Refinement stepCycle: LAST / Resolution: 4.90000680874→72.9250039452 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms41052 0 9192 0 50244
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0047823397204152088
X-RAY DIFFRACTIONf_angle_d0.75358379826971528
X-RAY DIFFRACTIONf_chiral_restr0.02935459929867238
X-RAY DIFFRACTIONf_plane_restr0.00403228326518510
X-RAY DIFFRACTIONf_dihedral_angle_d18.65239711418206
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
4.9-4.95970.348571252837960.3630845749152332X-RAY DIFFRACTION82.3050847458
4.9597-5.02250.3244624562011470.3635012069422483X-RAY DIFFRACTION87.9304580408
5.0225-5.08860.371917129161400.3636887962212584X-RAY DIFFRACTION90.5886265381
5.0886-5.15830.3709964013781420.3568448272512605X-RAY DIFFRACTION93.1502204137
5.1583-5.2320.3618870658241370.3477108305882642X-RAY DIFFRACTION94.2672998643
5.232-5.310.4123008600891410.346770330972756X-RAY DIFFRACTION95.6421261142
5.31-5.3930.3383009561991350.3474042577922671X-RAY DIFFRACTION95.9972630859
5.393-5.48140.334245421541400.3421920527972799X-RAY DIFFRACTION97.5116124751
5.4814-5.57580.353031330111450.3399134129052800X-RAY DIFFRACTION98.8586774085
5.5758-5.67720.3604205875311260.3237153611522813X-RAY DIFFRACTION99.8301630435
5.6772-5.78630.3684253411661710.330655431082825X-RAY DIFFRACTION99.8333888704
5.7863-5.90440.3387791490851400.3108141170262829X-RAY DIFFRACTION99.9663299663
5.9044-6.03270.3284299596011430.3065707616192839X-RAY DIFFRACTION100
6.0327-6.1730.3668242909511600.2992324434422794X-RAY DIFFRACTION99.9661590525
6.173-6.32730.3173545116851450.3038054055862842X-RAY DIFFRACTION100
6.3273-6.49830.2827564970481450.2860886602672820X-RAY DIFFRACTION100
6.4983-6.68930.3313988029221490.2845354774062822X-RAY DIFFRACTION100
6.6893-6.90510.2805834544531530.2769194023382840X-RAY DIFFRACTION100
6.9051-7.15170.3230193139781300.2586042256432844X-RAY DIFFRACTION100
7.1517-7.43780.2730229137891570.2596422738312819X-RAY DIFFRACTION100
7.4378-7.77590.304313458971370.2505448493172865X-RAY DIFFRACTION100
7.7759-8.18540.2814463118431510.2559877507292807X-RAY DIFFRACTION100
8.1854-8.69740.2312290446071560.2353250927882782X-RAY DIFFRACTION100
8.6974-9.36770.237302445241420.2265097063342855X-RAY DIFFRACTION100
9.3677-10.30810.2618507489471500.2277610055162833X-RAY DIFFRACTION100
10.3081-11.79420.2367572416451370.2191541753142824X-RAY DIFFRACTION99.9662390277
11.7942-14.83890.2169694953641530.2417960621742833X-RAY DIFFRACTION99.9665215936
14.8389-72.9330.2988778201371180.3273374487292859X-RAY DIFFRACTION100

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