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- PDB-7c52: Co-crystal structure of a photosynthetic LH1-RC in complex with e... -

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Basic information

Entry
Database: PDB / ID: 7c52
TitleCo-crystal structure of a photosynthetic LH1-RC in complex with electron donor HiPIP
Components
  • (Photosynthetic reaction center ...) x 4
  • High-potential iron-sulfur protein
  • LH1 alpha polypeptide
  • LH1 beta polypeptide
KeywordsPHOTOSYNTHESIS / LH1-RC / HiPIP / purple bacteria / electron transfer
Function / homology
Function and homology information


organelle inner membrane / aerobic electron transport chain / plasma membrane-derived chromatophore membrane / plasma membrane light-harvesting complex / bacteriochlorophyll binding / photosynthetic electron transport in photosystem II / photosynthesis, light reaction / photosynthesis / endomembrane system / 4 iron, 4 sulfur cluster binding ...organelle inner membrane / aerobic electron transport chain / plasma membrane-derived chromatophore membrane / plasma membrane light-harvesting complex / bacteriochlorophyll binding / photosynthetic electron transport in photosystem II / photosynthesis, light reaction / photosynthesis / endomembrane system / 4 iron, 4 sulfur cluster binding / electron transfer activity / iron ion binding / heme binding / metal ion binding / membrane / plasma membrane
Similarity search - Function
Light-harvesting complex / Light-harvesting Protein / High potential iron-sulfur protein / High potential iron-sulphur protein / High potential iron-sulphur protein superfamily / High potential iron-sulfur proteins family profile. / Photosynthetic reaction centre, cytochrome c subunit / Multihaem cytochrome, PRC subunit superfamily / Photosynthetic reaction centre cytochrome C subunit / Antenna complex, alpha subunit ...Light-harvesting complex / Light-harvesting Protein / High potential iron-sulfur protein / High potential iron-sulphur protein / High potential iron-sulphur protein superfamily / High potential iron-sulfur proteins family profile. / Photosynthetic reaction centre, cytochrome c subunit / Multihaem cytochrome, PRC subunit superfamily / Photosynthetic reaction centre cytochrome C subunit / Antenna complex, alpha subunit / Antenna complex, alpha subunit conserved site / Antenna complexes alpha subunits signature. / Photosynthetic Reaction Center; Chain H, domain 2 / Photosynthetic Reaction Center, subunit H, domain 2 / Multiheme cytochrome c family profile. / Antenna complex, alpha/beta subunit / Light-harvesting protein B beta chain / Antenna complex, beta domain superfamily / Antenna complex alpha/beta subunit / Light-harvesting complex / Photosynthetic reaction centre, H subunit / Bacterial photosynthetic reaction centre, H-chain, C-terminal / Photosynthetic reaction centre, H subunit, N-terminal / PRC-barrel domain / Photosynthetic reaction centre, H subunit, N-terminal domain superfamily / Photosynthetic reaction centre, H-chain N-terminal region / Photosynthetic reaction centre, M subunit / PRC-barrel domain / Photosynthetic reaction centre, L subunit / PRC-barrel-like superfamily / Multiheme cytochrome superfamily / : / Photosynthetic reaction centre, L/M / Photosystem II protein D1/D2 superfamily / Photosynthetic reaction centre protein / Photosynthetic reaction center proteins signature. / Few Secondary Structures / Irregular / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
BACTERIOCHLOROPHYLL A / BACTERIOPHEOPHYTIN A / CARDIOLIPIN / SPIRILLOXANTHIN / : / HEME C / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / MENAQUINONE 8 / DI-PALMITOYL-3-SN-PHOSPHATIDYLETHANOLAMINE / Chem-PGV ...BACTERIOCHLOROPHYLL A / BACTERIOPHEOPHYTIN A / CARDIOLIPIN / SPIRILLOXANTHIN / : / HEME C / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / MENAQUINONE 8 / DI-PALMITOYL-3-SN-PHOSPHATIDYLETHANOLAMINE / Chem-PGV / IRON/SULFUR CLUSTER / Ubiquinone-8 / Reaction center protein M chain / LH1 beta polypeptide / LH1 alpha polypeptide / Reaction center protein L chain / Photosynthetic reaction center cytochrome c subunit / Photosynthetic reaction center H subunit / High-potential iron-sulfur protein
Similarity search - Component
Biological speciesThermochromatium tepidum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.89 Å
AuthorsYu, L.-J. / Wang-Otomo, Z.-Y.
CitationJournal: Nat Commun / Year: 2021
Title: Crystal structure of a photosynthetic LH1-RC in complex with its electron donor HiPIP.
Authors: Kawakami, T. / Yu, L.J. / Liang, T. / Okazaki, K. / Madigan, M.T. / Kimura, Y. / Wang-Otomo, Z.Y.
History
DepositionMay 18, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 3, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Sep 17, 2025Group: Advisory / Derived calculations / Structure summary
Category: pdbx_entry_details / pdbx_modification_feature ...pdbx_entry_details / pdbx_modification_feature / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_close_contact / struct_conn
Item: _pdbx_entry_details.has_protein_modification
Revision 2.0Dec 17, 2025Group: Atomic model / Author supporting evidence ...Atomic model / Author supporting evidence / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / chem_comp_atom / chem_comp_bond / entity / pdbx_entity_instance_feature / pdbx_entity_nonpoly / pdbx_modification_feature / pdbx_nonpoly_scheme / pdbx_struct_conn_angle / struct_conn / struct_site / struct_site_gen
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.type_symbol / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.name / _chem_comp.pdbx_synonyms / _entity.formula_weight / _entity.pdbx_description / _pdbx_entity_instance_feature.auth_comp_id / _pdbx_entity_instance_feature.comp_id / _pdbx_entity_nonpoly.comp_id / _pdbx_entity_nonpoly.name / _pdbx_modification_feature.auth_comp_id / _pdbx_modification_feature.label_comp_id / _pdbx_modification_feature.ref_comp_id / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.pdb_mon_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_label_comp_id / _struct_site.details / _struct_site.pdbx_auth_comp_id / _struct_site_gen.auth_comp_id / _struct_site_gen.label_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: Photosynthetic reaction center cytochrome c subunit
L: Photosynthetic reaction center L subunit
M: Photosynthetic reaction center M subunit
H: Photosynthetic reaction center H subunit
A: LH1 alpha polypeptide
B: LH1 beta polypeptide
D: LH1 alpha polypeptide
E: LH1 beta polypeptide
F: LH1 alpha polypeptide
G: LH1 beta polypeptide
I: LH1 alpha polypeptide
J: LH1 beta polypeptide
K: LH1 alpha polypeptide
N: LH1 beta polypeptide
O: LH1 alpha polypeptide
P: LH1 beta polypeptide
Q: LH1 alpha polypeptide
R: LH1 beta polypeptide
S: LH1 alpha polypeptide
T: LH1 beta polypeptide
U: LH1 alpha polypeptide
V: LH1 beta polypeptide
W: LH1 alpha polypeptide
X: LH1 beta polypeptide
Y: LH1 alpha polypeptide
Z: LH1 beta polypeptide
1: LH1 alpha polypeptide
2: LH1 beta polypeptide
3: LH1 alpha polypeptide
4: LH1 beta polypeptide
5: LH1 alpha polypeptide
6: LH1 beta polypeptide
7: LH1 alpha polypeptide
8: LH1 beta polypeptide
9: LH1 alpha polypeptide
0: LH1 beta polypeptide
b: High-potential iron-sulfur protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)424,376157
Polymers340,64637
Non-polymers83,730120
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)96.435, 183.335, 123.857
Angle α, β, γ (deg.)90.000, 112.584, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
41
51
61
71
81
91
101
111
121
131
141
151
161
12
22
32
42
52
62
72
82
92
102
112
122
132
142
152
162

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain '0' and resid 9 through 101)09 - 46
121(chain '0' and resid 9 through 101)0101
211(chain '2' and resid 9 through 101)29 - 46
221(chain '2' and resid 9 through 101)2101
311(chain '4' and resid 9 through 101)49 - 46
321(chain '4' and resid 9 through 101)4101
411(chain '6' and resid 9 through 101)69 - 46
421(chain '6' and resid 9 through 101)6101
511(chain '8' and resid 9 through 101)89 - 46
521(chain '8' and resid 9 through 101)8101
611(chain 'B' and resid 9 through 101)B9 - 46
621(chain 'B' and resid 9 through 101)B101
711chain 'E'E9 - 46
721chain 'E'E101
811(chain 'G' and resid 9 through 101)G9 - 46
821(chain 'G' and resid 9 through 101)G101
911(chain 'J' and resid 9 through 101)J9 - 46
921(chain 'J' and resid 9 through 101)J101
1011(chain 'N' and resid 9 through 101)N9 - 46
1021(chain 'N' and resid 9 through 101)N101
1111(chain 'P' and resid 9 through 101)P9 - 46
1121(chain 'P' and resid 9 through 101)P101
1211(chain 'R' and resid 9 through 101)R9 - 46
1221(chain 'R' and resid 9 through 101)R101
1311(chain 'T' and resid 9 through 101)T9 - 46
1321(chain 'T' and resid 9 through 101)T101
1411(chain 'V' and resid 9 through 101)V9 - 46
1421(chain 'V' and resid 9 through 101)V101
1511(chain 'X' and resid 9 through 101)X9 - 46
1521(chain 'X' and resid 9 through 101)X101
1611(chain 'Z' and resid 9 through 101)Z9 - 46
1621(chain 'Z' and resid 9 through 101)Z101
112(chain '1' and (resid 6 through 29 or resid 31...16 - 29
122(chain '1' and (resid 6 through 29 or resid 31...131 - 36
132(chain '1' and (resid 6 through 29 or resid 31...138 - 40
142(chain '1' and (resid 6 through 29 or resid 31...142 - 58
152(chain '1' and (resid 6 through 29 or resid 31...1101 - 102
212(chain '3' and (resid 6 through 29 or resid 31...36 - 29
222(chain '3' and (resid 6 through 29 or resid 31...331 - 36
232(chain '3' and (resid 6 through 29 or resid 31...338 - 40
242(chain '3' and (resid 6 through 29 or resid 31...342 - 58
252(chain '3' and (resid 6 through 29 or resid 31...3101 - 102
312(chain '5' and (resid 6 through 29 or resid 31...56 - 29
322(chain '5' and (resid 6 through 29 or resid 31...531 - 36
332(chain '5' and (resid 6 through 29 or resid 31...538 - 40
342(chain '5' and (resid 6 through 29 or resid 31...542 - 58
352(chain '5' and (resid 6 through 29 or resid 31...5101 - 102
412(chain '7' and (resid 6 through 29 or resid 31...76 - 29
422(chain '7' and (resid 6 through 29 or resid 31...731 - 36
432(chain '7' and (resid 6 through 29 or resid 31...738 - 40
442(chain '7' and (resid 6 through 29 or resid 31...742 - 58
452(chain '7' and (resid 6 through 29 or resid 31...7101 - 102
512(chain '9' and (resid 6 through 29 or resid 31...96 - 29
522(chain '9' and (resid 6 through 29 or resid 31...931 - 36
532(chain '9' and (resid 6 through 29 or resid 31...938 - 40
542(chain '9' and (resid 6 through 29 or resid 31...942 - 58
552(chain '9' and (resid 6 through 29 or resid 31...9101 - 102
612(chain 'A' and (resid 6 through 29 or resid 31...A6 - 29
622(chain 'A' and (resid 6 through 29 or resid 31...A31 - 36
632(chain 'A' and (resid 6 through 29 or resid 31...A38 - 40
642(chain 'A' and (resid 6 through 29 or resid 31...A42 - 58
652(chain 'A' and (resid 6 through 29 or resid 31...A101 - 102
712(chain 'D' and (resid 6 through 29 or resid 31...D6 - 29
722(chain 'D' and (resid 6 through 29 or resid 31...D31 - 36
732(chain 'D' and (resid 6 through 29 or resid 31...D38 - 40
742(chain 'D' and (resid 6 through 29 or resid 31...D42 - 58
752(chain 'D' and (resid 6 through 29 or resid 31...D101 - 102
812(chain 'F' and (resid 6 through 29 or resid 31...F6 - 29
822(chain 'F' and (resid 6 through 29 or resid 31...F31 - 36
832(chain 'F' and (resid 6 through 29 or resid 31...F38 - 40
842(chain 'F' and (resid 6 through 29 or resid 31...F42 - 58
852(chain 'F' and (resid 6 through 29 or resid 31...F101 - 102
912(chain 'I' and (resid 6 through 29 or resid 31...I6 - 29
922(chain 'I' and (resid 6 through 29 or resid 31...I31 - 36
932(chain 'I' and (resid 6 through 29 or resid 31...I38 - 40
942(chain 'I' and (resid 6 through 29 or resid 31...I42 - 58
952(chain 'I' and (resid 6 through 29 or resid 31...I101 - 102
1012(chain 'K' and (resid 6 through 29 or resid 31...K6 - 29
1022(chain 'K' and (resid 6 through 29 or resid 31...K31 - 36
1032(chain 'K' and (resid 6 through 29 or resid 31...K38 - 40
1042(chain 'K' and (resid 6 through 29 or resid 31...K42 - 58
1052(chain 'K' and (resid 6 through 29 or resid 31...K101 - 102
1112(chain 'O' and (resid 6 through 29 or resid 31...O6 - 29
1122(chain 'O' and (resid 6 through 29 or resid 31...O31 - 36
1132(chain 'O' and (resid 6 through 29 or resid 31...O38 - 40
1142(chain 'O' and (resid 6 through 29 or resid 31...O42 - 58
1152(chain 'O' and (resid 6 through 29 or resid 31...O101 - 102
1212(chain 'Q' and (resid 6 through 29 or resid 31...Q6 - 29
1222(chain 'Q' and (resid 6 through 29 or resid 31...Q31 - 36
1232(chain 'Q' and (resid 6 through 29 or resid 31...Q38 - 40
1242(chain 'Q' and (resid 6 through 29 or resid 31...Q42 - 58
1252(chain 'Q' and (resid 6 through 29 or resid 31...Q101 - 102
1312(chain 'S' and (resid 6 through 29 or resid 31...S6 - 29
1322(chain 'S' and (resid 6 through 29 or resid 31...S31 - 36
1332(chain 'S' and (resid 6 through 29 or resid 31...S38 - 40
1342(chain 'S' and (resid 6 through 29 or resid 31...S42 - 58
1352(chain 'S' and (resid 6 through 29 or resid 31...S101 - 102
1412(chain 'U' and (resid 6 through 29 or resid 31...U6 - 29
1422(chain 'U' and (resid 6 through 29 or resid 31...U31 - 36
1432(chain 'U' and (resid 6 through 29 or resid 31...U38 - 40
1442(chain 'U' and (resid 6 through 29 or resid 31...U42 - 58
1452(chain 'U' and (resid 6 through 29 or resid 31...U101 - 102
1512(chain 'W' and (resid 6 through 29 or resid 31...W6 - 29
1522(chain 'W' and (resid 6 through 29 or resid 31...W31 - 36
1532(chain 'W' and (resid 6 through 29 or resid 31...W38 - 40
1542(chain 'W' and (resid 6 through 29 or resid 31...W42 - 58
1552(chain 'W' and (resid 6 through 29 or resid 31...W101 - 102
1612(chain 'Y' and (resid 6 through 29 or resid 31...Y6 - 29
1622(chain 'Y' and (resid 6 through 29 or resid 31...Y31 - 36
1632(chain 'Y' and (resid 6 through 29 or resid 31...Y38 - 40
1642(chain 'Y' and (resid 6 through 29 or resid 31...Y42 - 58
1652(chain 'Y' and (resid 6 through 29 or resid 31...Y101 - 102

NCS ensembles :
ID
1
2

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Components

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Photosynthetic reaction center ... , 4 types, 4 molecules CLMH

#1: Protein Photosynthetic reaction center cytochrome c subunit


Mass: 34409.754 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermochromatium tepidum (bacteria) / References: UniProt: D2Z0P5
#2: Protein Photosynthetic reaction center L subunit


Mass: 31520.771 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermochromatium tepidum (bacteria) / References: UniProt: D2Z0P3
#3: Protein Photosynthetic reaction center M subunit


Mass: 36605.715 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermochromatium tepidum (bacteria) / References: UniProt: A8ASG6
#4: Protein Photosynthetic reaction center H subunit


Mass: 28213.305 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermochromatium tepidum (bacteria) / References: UniProt: D2Z0P9

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Protein , 2 types, 17 molecules ADFIKOQSUWY13579b

#5: Protein
LH1 alpha polypeptide


Mass: 7034.442 Da / Num. of mol.: 16 / Source method: isolated from a natural source / Source: (natural) Thermochromatium tepidum (bacteria) / References: UniProt: D2Z0P2
#7: Protein High-potential iron-sulfur protein / HiPIP


Mass: 8793.851 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermochromatium tepidum (bacteria) / References: UniProt: P80176

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Protein/peptide / Sugars , 2 types, 18 molecules BEGJNPRTVXZ24680

#22: Sugar ChemComp-LMT / DODECYL-BETA-D-MALTOSIDE


Type: D-saccharide / Mass: 510.615 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C24H46O11 / Comment: detergent*YM
#6: Protein/peptide
LH1 beta polypeptide


Mass: 5534.452 Da / Num. of mol.: 16 / Source method: isolated from a natural source / Source: (natural) Thermochromatium tepidum (bacteria) / References: UniProt: D2Z0P1

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Non-polymers , 15 types, 118 molecules

#8: Chemical
ChemComp-HEC / HEME C


Mass: 618.503 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H34FeN4O4 / Feature type: SUBJECT OF INVESTIGATION
#9: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: Ca
#10: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#11: Chemical ChemComp-LHG / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE


Mass: 722.970 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C38H75O10P / Comment: phospholipid*YM
#12: Chemical
ChemComp-PGV / (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE / PHOSPHATIDYLGLYCEROL / 2-VACCENOYL-1-PALMITOYL-SN-GLYCEROL-3-PHOSPHOGLYCEROL


Mass: 749.007 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C40H77O10P / Comment: phospholipid*YM
#13: Chemical...
ChemComp-BCL / BACTERIOCHLOROPHYLL A


Mass: 911.504 Da / Num. of mol.: 36 / Source method: obtained synthetically / Formula: C55H74MgN4O6
#14: Chemical ChemComp-BPH / BACTERIOPHEOPHYTIN A


Mass: 889.215 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C55H76N4O6
#15: Chemical
ChemComp-UQ8 / Ubiquinone-8 / 2,3-dimethoxy-5-methyl-6-[(6E,10E,14E,18E,22E,26E)-3,7,11,15,19,23,27,31-octamethyldotriaconta-2,6,10,14,18,22,26,30-oc taen-1-yl]cyclohexa-2,5-diene-1,4-dione


Mass: 727.109 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C49H74O4
#16: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#17: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#18: Chemical ChemComp-MQ8 / MENAQUINONE 8 / 2-METHYL-3-(3,7,11,15,19,23,27,31-OCTAMETHYL-DOTRIACONTA-2,6,10,14,18,22,26,30-OCTAENYL)-[1,4]NAPTHOQUINONE


Mass: 717.116 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C51H72O2
#19: Chemical
ChemComp-CRT / SPIRILLOXANTHIN / RHODOVIOLASCIN


Mass: 596.925 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: C42H60O2
#20: Chemical
ChemComp-CDL / CARDIOLIPIN / DIPHOSPHATIDYL GLYCEROL / BIS-(1,2-DIACYL-SN-GLYCERO-3-PHOSPHO)-1',3'-SN-GLYCEROL


Mass: 1464.043 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C81H156O17P2 / Comment: phospholipid*YM
#21: Chemical
ChemComp-PEF / DI-PALMITOYL-3-SN-PHOSPHATIDYLETHANOLAMINE / 3-[AMINOETHYLPHOSPHORYL]-[1,2-DI-PALMITOYL]-SN-GLYCEROL


Mass: 691.959 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C37H74NO8P / Comment: phospholipid*YM
#23: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe4S4 / Feature type: SUBJECT OF INVESTIGATION

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Details

Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.97 Å3/Da / Density meas: 51.36 Mg/m3 / Density % sol: 52.8 %
Crystal growTemperature: 293 K / Method: batch mode / pH: 5 / Details: PEG 1500, sodium succinate, calcium chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 13, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.89→48.2 Å / Num. obs: 86259 / % possible obs: 97.4 % / Redundancy: 6.5 % / Biso Wilson estimate: 103.66 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.127 / Net I/σ(I): 10.3
Reflection shellResolution: 2.893→2.996 Å / Rmerge(I) obs: 2.06 / Mean I/σ(I) obs: 0.69 / Num. unique obs: 6927 / CC1/2: 0.334 / % possible all: 87.7

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Processing

Software
NameVersionClassification
XDSMay 1, 2016data reduction
XDSMay 1, 2016data scaling
PHASER2.7.16phasing
Coot0.8.8model building
PHENIX1.17.1_3660refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5Y5S

5y5s


Resolution: 2.89→29.99 Å / SU ML: 0.5015 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 29.3974
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2477 4311 5 %
Rwork0.2188 81948 -
obs0.2203 86259 97.57 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 128.67 Å2
Refinement stepCycle: LAST / Resolution: 2.89→29.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms26183 0 1165 0 27348
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.005528419
X-RAY DIFFRACTIONf_angle_d1.232239065
X-RAY DIFFRACTIONf_chiral_restr0.05984015
X-RAY DIFFRACTIONf_plane_restr0.00814694
X-RAY DIFFRACTIONf_dihedral_angle_d21.05410283
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.89-2.930.4432840.39861619X-RAY DIFFRACTION57.98
2.93-2.960.37481270.37582412X-RAY DIFFRACTION85.69
2.96-30.40461340.35762551X-RAY DIFFRACTION92.36
3-3.030.37191450.34272747X-RAY DIFFRACTION97.54
3.03-3.070.33621430.33352718X-RAY DIFFRACTION99
3.07-3.120.38061490.34512826X-RAY DIFFRACTION99.66
3.12-3.160.3871440.33462745X-RAY DIFFRACTION100
3.16-3.210.39251490.33182834X-RAY DIFFRACTION100
3.21-3.260.34651470.31542788X-RAY DIFFRACTION99.93
3.26-3.310.35371460.28682772X-RAY DIFFRACTION99.93
3.31-3.370.27751470.27552792X-RAY DIFFRACTION99.86
3.37-3.430.29441460.26682780X-RAY DIFFRACTION99.69
3.43-3.50.30241460.2692758X-RAY DIFFRACTION99.83
3.5-3.570.29761490.25142846X-RAY DIFFRACTION99.97
3.57-3.640.28751460.25332761X-RAY DIFFRACTION99.79
3.64-3.730.31611450.23972769X-RAY DIFFRACTION99.79
3.73-3.820.29921490.23632827X-RAY DIFFRACTION99.93
3.82-3.920.26171450.22372752X-RAY DIFFRACTION99.72
3.92-4.040.21681480.20772815X-RAY DIFFRACTION99.7
4.04-4.170.23231480.20322812X-RAY DIFFRACTION99.73
4.17-4.320.21041460.19332763X-RAY DIFFRACTION99.83
4.32-4.490.23141460.19142791X-RAY DIFFRACTION99.69
4.49-4.690.22141470.18392786X-RAY DIFFRACTION99.69
4.69-4.940.20241470.17432798X-RAY DIFFRACTION99.46
4.94-5.250.21411460.1832785X-RAY DIFFRACTION99.69
5.25-5.650.23171490.18582827X-RAY DIFFRACTION99.83
5.65-6.220.27261470.20352798X-RAY DIFFRACTION99.86
6.22-7.10.18561470.18662800X-RAY DIFFRACTION99.8
7.11-8.910.19731500.1792835X-RAY DIFFRACTION99.7
8.91-29.990.23641490.22432841X-RAY DIFFRACTION99.43
Refinement TLS params.Method: refined / Origin x: -20.4225777797 Å / Origin y: 30.0155694781 Å / Origin z: 134.549072079 Å
111213212223313233
T0.639274510059 Å20.154187999037 Å20.0665090030576 Å2-0.720829025336 Å2-0.0554073202315 Å2--0.632260323799 Å2
L1.30074596768 °2-0.79111332594 °20.234168156031 °2-1.86953965519 °2-0.302349271942 °2--0.895255011268 °2
S-0.0108308414687 Å °0.0050683037848 Å °0.0465939237767 Å °-0.0104805142381 Å °-0.0236168342446 Å °0.048696689026 Å °-0.0636343721319 Å °-0.042243731464 Å °0.0312277969869 Å °
Refinement TLS groupSelection details: all

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