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- PDB-4pbu: Serial Time-resolved crystallography of Photosystem II using a fe... -

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Basic information

Entry
Database: PDB / ID: 4pbu
TitleSerial Time-resolved crystallography of Photosystem II using a femtosecond X-ray laser The S1 state
Components
  • (Cytochrome b559 subunit ...) x 2
  • (Photosystem II ...) x 15
  • Cytochrome c-550
  • Photosystem Q(B) protein 1
KeywordsPHOTOSYNTHESIS / Photosystem II / Time resolved / Free electron laser
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 / 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 reaction centre protein Ycf12 ...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) / : / PROTOPORPHYRIN IX CONTAINING FE / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / CA-MN4-O5 CLUSTER / PHEOPHYTIN A / Chem-PL9 ...BETA-CAROTENE / BICARBONATE ION / CHLOROPHYLL A / DIGALACTOSYL DIACYL GLYCEROL (DGDG) / : / PROTOPORPHYRIN IX CONTAINING FE / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / 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 / molecular replacement / Resolution: 5 Å
AuthorsKupitz, C. / Basu, S. / Grotjohann, I. / Fromme, R. / Zatsepin, N. / Rendek, K.N. / Hunter, M. / Shoeman, R.L. / White, T.A. / Wang, D. ...Kupitz, C. / Basu, S. / Grotjohann, I. / Fromme, R. / Zatsepin, N. / Rendek, K.N. / Hunter, M. / Shoeman, R.L. / White, T.A. / Wang, D. / James, D. / Yang, J.H. / Cobb, D.E. / Reeder, B. / Sierra, R.G. / Liu, H. / Barty, A. / Aquila, A. / Deponte, D. / Kirian, R.A. / Bari, S. / Bergkamp, J.J. / Beyerlein, K. / Bogan, M.J. / Caleman, C. / Chao, T.-C. / Conrad, C.E. / Davis, K.M. / Fleckenstein, H. / Galli, L. / Hau-Riege, S.P. / Kassemeyer, S. / Laksmono, H. / Liang, M. / Lomb, L. / Marchesini, S. / Martin, A.V. / Messerschmidt, M. / Milathianaki, D. / Nass, K. / Ros, A. / Roy-Chowdhury, S. / Schmidt, K. / Seibert, M. / Steinbrener, J. / Stellato, F. / Yan, L. / Yoon, C. / Moore, T.A. / Moore, A.L. / Pushkar, Y. / Williams, G.J. / Boutet, S. / Doak, R.B. / Weierstall, U. / Frank, M. / Chapman, H.N. / Spence, J.C.H. / Fromme, P.
Funding support United States, Germany, 14items
OrganizationGrant numberCountry
Department of Energy (DOE, United States)DE-SC0001016 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1R01GM095583 United States
National Science Foundation (NSF, United States)MCB-1021557 United States
National Science Foundation (NSF, United States)MCB- 1120997 United States
German Research Foundation (DFG)EXC 306 Germany
German Research Foundation (DFG)?Center for Ultrafast Imaging? Germany
Max Planck SocietyAtomic, Molecular and Optical Sciences Program Germany
Department of Energy (DOE, United States)Chemical Sciences Geosciences and Biosciences Division United States
SLACLDRD United States
Department of Energy (DOE, United States)DE-AC52- 07NA27344 United States
UCOP Lab Fee Program118036 United States
LLNL LDRD12-ERD-031 United States
Hamburg Initiative for Excellence in ResearchHamburg Ministry of Science and Research and Joachim Herz Stiftung Germany
National Science Foundation (NSF, United States)BioFEL Science Technology Center (award 1231306) United States
CitationJournal: Nature / Year: 2014
Title: Serial time-resolved crystallography of photosystem II using a femtosecond X-ray laser.
Authors: Kupitz, C. / Basu, S. / Grotjohann, I. / Fromme, R. / Zatsepin, N.A. / Rendek, K.N. / Hunter, M.S. / Shoeman, R.L. / White, T.A. / Wang, D. / James, D. / Yang, J.H. / Cobb, D.E. / Reeder, B. ...Authors: Kupitz, C. / Basu, S. / Grotjohann, I. / Fromme, R. / Zatsepin, N.A. / Rendek, K.N. / Hunter, M.S. / Shoeman, R.L. / White, T.A. / Wang, D. / James, D. / Yang, J.H. / Cobb, D.E. / Reeder, B. / Sierra, R.G. / Liu, H. / Barty, A. / Aquila, A.L. / Deponte, D. / Kirian, R.A. / Bari, S. / Bergkamp, J.J. / Beyerlein, K.R. / Bogan, M.J. / Caleman, C. / Chao, T.C. / Conrad, C.E. / Davis, K.M. / Fleckenstein, H. / Galli, L. / Hau-Riege, S.P. / Kassemeyer, S. / Laksmono, H. / Liang, M. / Lomb, L. / Marchesini, S. / Martin, A.V. / Messerschmidt, M. / Milathianaki, D. / Nass, K. / Ros, A. / Roy-Chowdhury, S. / Schmidt, K. / Seibert, M. / Steinbrener, J. / Stellato, F. / Yan, L. / Yoon, C. / Moore, T.A. / Moore, A.L. / Pushkar, Y. / Williams, G.J. / Boutet, S. / Doak, R.B. / Weierstall, U. / Frank, M. / Chapman, H.N. / Spence, J.C. / Fromme, P.
History
DepositionApr 13, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 16, 2014Provider: repository / Type: Initial release
Revision 1.1Jul 30, 2014Group: Database references
Revision 1.2Aug 6, 2014Group: Structure summary
Revision 1.3Oct 1, 2014Group: Database references
Revision 1.4Sep 23, 2015Group: Data collection
Revision 1.5Sep 6, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.6Nov 22, 2017Group: Refinement description / Category: software
Revision 1.7Sep 19, 2018Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.detector
Revision 1.8Nov 27, 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_struct_conn_angle / pdbx_validate_chiral / struct_conn / struct_conn_type
Item: _chem_comp.formula / _database_2.pdbx_DOI ..._chem_comp.formula / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_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.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_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 / _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.ptnr2_symmetry / _struct_conn_type.id

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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
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
y: Photosystem II reaction center protein Ycf12
x: Photosystem II reaction center X protein
z: Photosystem II reaction center protein Z
hetero molecules


Theoretical massNumber of molelcules
Total (without water)692,590190
Polymers584,77338
Non-polymers107,818152
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)133.250, 226.260, 307.090
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
11chain A
21chain a
12chain B
22chain b
13chain C
23chain c
14chain D
24chain d
15chain E
25chain e
16chain F
26chain f
17chain H
27chain h
18chain I
28chain i
19chain J
29chain j
110chain K
210chain k
111chain L
211chain l
112chain M
212chain m
113chain O
213chain o
114chain T
214chain t
115chain U
215chain u
116chain V
216chain v
117chain X
217chain x
118chain Y
218chain y
119chain Z
219chain z

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111chain AA11 - 667
211chain aa11 - 659
112chain BB2 - 668
212chain bb2 - 649
113chain CC23 - 661
213chain cc19 - 661
114chain DD11 - 714
214chain dd12 - 714
115chain EE4 - 772
215chain ee4 - 772
116chain FF12 - 641
216chain ff14 - 641
117chain HH2 - 663
217chain hh2 - 663
118chain II1 - 38
218chain ii1 - 38
119chain JJ3 - 40
219chain jj1 - 652
1110chain KK10 - 653
2110chain kk10 - 653
1111chain LL1 - 668
2111chain ll1 - 694
1112chain MM1 - 34
2112chain mm1 - 34
1113chain OO4 - 767
2113chain oo4 - 767
1114chain TT1 - 647
2114chain tt1 - 647
1115chain UU8 - 808
2115chain uu8 - 104
1116chain VV1 - 642
2116chain vv1 - 642
1117chain XX2 - 40
2117chain xx2 - 40
1118chain YY18 - 46
2118chain yy18 - 46
1119chain ZZ1 - 62
2119chain zz1 - 62

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 D-1 / Photosystem II D-1 protein


Mass: 37029.234 Da / Num. of mol.: 2 / 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: 15148.255 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 ... , 15 types, 30 molecules BbCcDdHhIiJjKkLlMmOoTtUuYyXxZz

#2: Protein Photosystem II core light harvesting protein / / Photosystem II CP47 protein


Mass: 55939.562 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: 49668.758 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 / Photosystem II D2 protein


Mass: 38404.949 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: 7227.559 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: 4101.911 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: 3807.517 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: 26523.578 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: 3620.369 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: 10966.317 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: 3098.921 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: 4077.873 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 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: 9321.515 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: 3868.611 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 , 1 types, 10 molecules

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


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

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Non-polymers , 13 types, 142 molecules

#20: Chemical ChemComp-OEX / CA-MN4-O5 CLUSTER


Mass: 339.827 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CaMn4O5
#21: Chemical ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe
#22: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cl
#23: Chemical ChemComp-BCT / BICARBONATE ION / Bicarbonate


Mass: 61.017 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CHO3 / Comment: pH buffer*YM
#24: Chemical...
ChemComp-CLA / CHLOROPHYLL A / Chlorophyll a


Mass: 893.489 Da / Num. of mol.: 70 / Source method: obtained synthetically / Formula: C55H72MgN4O5
#25: Chemical
ChemComp-PHO / PHEOPHYTIN A / Pheophytin


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


Mass: 536.873 Da / Num. of mol.: 22 / Source method: obtained synthetically / Formula: C40H56
#27: 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
#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
#30: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Ca
#32: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


Mass: 616.487 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#33: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg

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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: 3.96 Å3/Da / Density % sol: 68.92 %
Crystal growTemperature: 283 K / Method: liquid diffusion / pH: 7
Details: 100 mM Pipes pH 7.0, 5 mM CaCl2, 10 mM tocopherol, and 10-17% PEG 2000

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: FREE ELECTRON LASER / Site: SLAC LCLS / Beamline: CXI / Wavelength: 2.04 Å
DetectorType: CS-PAD CXI-2 / Detector: PIXEL / Date: Jan 25, 2012 / Details: several days
RadiationMonochromator: None / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 2.04 Å / Relative weight: 1
ReflectionResolution: 5→100.638 Å / Num. all: 41704 / Num. obs: 40964 / % possible obs: 100 % / Redundancy: 684 % / Biso Wilson estimate: 285.07 Å2 / Net I/σ(I): 5.4
Reflection shellResolution: 5→5.123 Å / Redundancy: 617 % / Mean I/σ(I) obs: 2.1 / % possible all: 99

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassification
Cheetahdata collection
CrystFELdata reduction
PDB_EXTRACT3.14data extraction
PHASERphasing
PHENIX(phenix.refine: 1.8.2_1309)refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3ARC

3arc
PDB Unreleased entry


Resolution: 5→100.638 Å / SU ML: 0.6 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 26.72 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.262 2056 5.02 %
Rwork0.2606 38890 -
obs0.2607 40946 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 111.03 Å2 / Biso mean: 33.7489 Å2 / Biso min: 13.83 Å2
Refinement stepCycle: final / Resolution: 5→100.638 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms41296 0 7625 0 48921
Biso mean--37.34 --
Num. residues----5270
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.03951301
X-RAY DIFFRACTIONf_angle_d3.02970757
X-RAY DIFFRACTIONf_chiral_restr0.4917125
X-RAY DIFFRACTIONf_plane_restr0.028628
X-RAY DIFFRACTIONf_dihedral_angle_d21.65918204
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A3021X-RAY DIFFRACTION7.008TORSIONAL
12a3021X-RAY DIFFRACTION7.008TORSIONAL
21B4445X-RAY DIFFRACTION7.008TORSIONAL
22b4445X-RAY DIFFRACTION7.008TORSIONAL
31C4054X-RAY DIFFRACTION7.008TORSIONAL
32c4054X-RAY DIFFRACTION7.008TORSIONAL
41D3154X-RAY DIFFRACTION7.008TORSIONAL
42d3154X-RAY DIFFRACTION7.008TORSIONAL
51E735X-RAY DIFFRACTION7.008TORSIONAL
52e735X-RAY DIFFRACTION7.008TORSIONAL
61F290X-RAY DIFFRACTION7.008TORSIONAL
62f290X-RAY DIFFRACTION7.008TORSIONAL
71H568X-RAY DIFFRACTION7.008TORSIONAL
72h568X-RAY DIFFRACTION7.008TORSIONAL
81I342X-RAY DIFFRACTION7.008TORSIONAL
82i342X-RAY DIFFRACTION7.008TORSIONAL
91J312X-RAY DIFFRACTION7.008TORSIONAL
92j312X-RAY DIFFRACTION7.008TORSIONAL
101K336X-RAY DIFFRACTION7.008TORSIONAL
102k336X-RAY DIFFRACTION7.008TORSIONAL
111L348X-RAY DIFFRACTION7.008TORSIONAL
112l348X-RAY DIFFRACTION7.008TORSIONAL
121M302X-RAY DIFFRACTION7.008TORSIONAL
122m302X-RAY DIFFRACTION7.008TORSIONAL
131O2194X-RAY DIFFRACTION7.008TORSIONAL
132o2194X-RAY DIFFRACTION7.008TORSIONAL
141T273X-RAY DIFFRACTION7.008TORSIONAL
142t273X-RAY DIFFRACTION7.008TORSIONAL
151U930X-RAY DIFFRACTION7.008TORSIONAL
152u930X-RAY DIFFRACTION7.008TORSIONAL
161V1264X-RAY DIFFRACTION7.008TORSIONAL
162v1264X-RAY DIFFRACTION7.008TORSIONAL
171X313X-RAY DIFFRACTION7.008TORSIONAL
172x313X-RAY DIFFRACTION7.008TORSIONAL
181Y251X-RAY DIFFRACTION7.008TORSIONAL
182y251X-RAY DIFFRACTION7.008TORSIONAL
191Z531X-RAY DIFFRACTION7.008TORSIONAL
192z531X-RAY DIFFRACTION7.008TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 15 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
5-5.11630.34341400.350225702710
5.1163-5.24420.36321340.324625322666
5.2442-5.3860.29851330.31225642697
5.386-5.54450.28341380.30825592697
5.5445-5.72350.28061280.295925312659
5.7235-5.9280.25171350.285925672702
5.928-6.16530.27311440.276625692713
6.1653-6.44590.25091360.260125792715
6.4459-6.78560.25031600.245425332693
6.7856-7.21070.24251160.240726172733
7.2107-7.76720.22211180.23626342752
7.7672-8.54850.20551350.207125882723
8.5485-9.78460.17191520.191626172769
9.7846-12.3240.21831460.202126492795
12.324-100.65830.34921410.330827812922

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