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- PDB-5oy0: Structure of synechocystis photosystem I trimer at 2.5A resolution -

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Basic information

Entry
Database: PDB / ID: 5oy0
TitleStructure of synechocystis photosystem I trimer at 2.5A resolution
Components
  • (Photosystem I P700 chlorophyll a apoprotein ...) x 4
  • (Photosystem I iron-sulfur ...) x 2
  • (Photosystem I reaction center subunit ...) x 14
KeywordsPHOTOSYNTHESIS / photosystem I / reaction center / cyanobacteria / electron transfer chain / synechocystis
Function / homology
Function and homology information


photosystem I reaction center / photosystem I / photosynthetic electron transport in photosystem I / photosystem I / chlorophyll binding / plasma membrane-derived thylakoid membrane / photosynthesis / 4 iron, 4 sulfur cluster binding / electron transfer activity / oxidoreductase activity ...photosystem I reaction center / photosystem I / photosynthetic electron transport in photosystem I / photosystem I / chlorophyll binding / plasma membrane-derived thylakoid membrane / photosynthesis / 4 iron, 4 sulfur cluster binding / electron transfer activity / oxidoreductase activity / magnesium ion binding / metal ion binding / plasma membrane
Similarity search - Function
Photosystem I, reaction centre, subunit PsaF / Photosystem I p700 chlorophyll A apoprotein A1 / Photosystem I PsaA/PsaB / Photosystem 1 Reaction Centre Subunit Ii; Chain: D; / Photosystem I PsaD, reaction center subunit II / Photosystem 1 Reaction Centre Subunit Xi; Chain: L; / Photosystem I PsaL, reaction centre subunit XI / Single helix bin / Photosystem I reaction center subunit PsaK / Photosystem I reaction centre subunit PsaK ...Photosystem I, reaction centre, subunit PsaF / Photosystem I p700 chlorophyll A apoprotein A1 / Photosystem I PsaA/PsaB / Photosystem 1 Reaction Centre Subunit Ii; Chain: D; / Photosystem I PsaD, reaction center subunit II / Photosystem 1 Reaction Centre Subunit Xi; Chain: L; / Photosystem I PsaL, reaction centre subunit XI / Single helix bin / Photosystem I reaction center subunit PsaK / Photosystem I reaction centre subunit PsaK / SH3 type barrels. - #50 / Photosystem I PsaM, reaction centre superfamily / Photosystem I PsaM, reaction centre / Photosystem I protein M (PsaM) / Photosystem I reaction centre subunit PsaK superfamily / Photosystem I psaG and psaK proteins signature. / Photosystem I reaction center subunit V/PsaK / Photosystem I psaG / psaK / Photosystem I PsaL, reaction centre subunit XI / Photosystem I, reaction centre subunit XI / Photosystem I PsaL, reaction centre subunit XI superfamily / Photosystem I reaction centre subunit XI / Photosystem I reaction centre subunit VIII / Photosystem I reaction centre subunit VIII / Photosystem I reaction centre subunit VIII superfamily / Photosystem I PsaF, reaction centre subunit III / Photosystem I PsaF, reaction centre subunit III superfamily / Photosystem I reaction centre subunit III / Alpha-Beta Plaits - #20 / Photosystem I PsaD / Photosystem I, reaction centre subunit PsaD superfamily / PsaD / Photosystem I PsaE, reaction centre subunit IV / Photosystem I PsaJ, reaction centre subunit IX superfamily / Photosystem I reaction centre subunit IV / PsaE / Photosystem I PsaJ, reaction centre subunit IX / Photosystem I reaction centre subunit IX / PsaJ / Photosystem I protein PsaC / Photosystem I PsaB / Photosystem I PsaA / Photosystem I PsaA/PsaB, conserved site / Photosystem I psaA and psaB proteins signature. / : / Photosystem I PsaA/PsaB / Photosystem I PsaA/PsaB superfamily / Photosystem I psaA/psaB protein / Electron transport accessory-like domain superfamily / 4Fe-4S dicluster domain / Helicase, Ruva Protein; domain 3 / 4Fe-4S ferredoxin, iron-sulphur binding, conserved site / 4Fe-4S ferredoxin-type iron-sulfur binding region signature. / 4Fe-4S ferredoxin-type iron-sulfur binding domain profile. / 4Fe-4S ferredoxin-type, iron-sulphur binding domain / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / SH3 type barrels. / Roll / Alpha-Beta Plaits / Up-down Bundle / 2-Layer Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
beta,beta-carotene-4,4'-dione / ACETATE ION / BETA-CAROTENE / CHLOROPHYLL A / DIGALACTOSYL DIACYL GLYCEROL (DGDG) / beta,beta-caroten-4-one / (3'R)-3'-hydroxy-beta,beta-caroten-4-one / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / PHYLLOQUINONE ...beta,beta-carotene-4,4'-dione / ACETATE ION / BETA-CAROTENE / CHLOROPHYLL A / DIGALACTOSYL DIACYL GLYCEROL (DGDG) / beta,beta-caroten-4-one / (3'R)-3'-hydroxy-beta,beta-caroten-4-one / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / PHYLLOQUINONE / IRON/SULFUR CLUSTER / Chem-SQD / Chem-ZEX / Photosystem I reaction center subunit IV / Photosystem I reaction center subunit II / Photosystem I P700 chlorophyll a apoprotein A1 / Photosystem I P700 chlorophyll a apoprotein A2 / Photosystem I reaction center subunit III / Photosystem I iron-sulfur center / Photosystem I reaction center subunit XI / Photosystem I reaction center subunit XII / Photosystem I reaction center subunit PsaK 2 / Photosystem I reaction center subunit IX / Photosystem I reaction center subunit VIII
Similarity search - Component
Biological speciesSynechocystis sp. PCC 6803 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.501 Å
AuthorsNelson, N. / Malavath, T. / Caspy, I.
Funding support Belgium, Israel, 2items
OrganizationGrant numberCountry
European Research Council293579 Belgium
ISF71/14 Israel
CitationJournal: Biochim. Biophys. Acta / Year: 2018
Title: Structure and function of wild-type and subunit-depleted photosystem I in Synechocystis.
Authors: Malavath, T. / Caspy, I. / Netzer-El, S.Y. / Klaiman, D. / Nelson, N.
History
DepositionSep 7, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 21, 2018Provider: repository / Type: Initial release
Revision 1.1Aug 15, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 2.0Oct 23, 2019Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Non-polymer description / Source and taxonomy / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_PDB_caveat / entity / entity_src_nat / pdbx_distant_solvent_atoms / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_chiral / pdbx_validate_close_contact / struct_asym / 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_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.occupancy / _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 / _entity.pdbx_description / _entity_src_nat.pdbx_ncbi_taxonomy_id / _entity_src_nat.pdbx_organism_scientific / _entity_src_nat.strain / _pdbx_distant_solvent_atoms.auth_seq_id / _pdbx_entity_nonpoly.comp_id / _pdbx_entity_nonpoly.name / _pdbx_nonpoly_scheme.auth_mon_id / _pdbx_nonpoly_scheme.auth_seq_num / _pdbx_nonpoly_scheme.entity_id / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.pdb_mon_id / _pdbx_nonpoly_scheme.pdb_seq_num / _pdbx_nonpoly_scheme.pdb_strand_id / _pdbx_unobs_or_zero_occ_atoms.auth_asym_id / _pdbx_unobs_or_zero_occ_atoms.auth_atom_id / _pdbx_unobs_or_zero_occ_atoms.auth_comp_id / _pdbx_unobs_or_zero_occ_atoms.auth_seq_id / _pdbx_unobs_or_zero_occ_atoms.label_asym_id / _pdbx_unobs_or_zero_occ_atoms.label_atom_id / _pdbx_unobs_or_zero_occ_atoms.label_comp_id / _struct_asym.entity_id / _struct_site.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id / _struct_site.pdbx_num_residues / _struct_site_gen.auth_asym_id / _struct_site_gen.auth_comp_id / _struct_site_gen.auth_seq_id / _struct_site_gen.label_asym_id / _struct_site_gen.label_comp_id / _struct_site_gen.label_seq_id / _struct_site_gen.pdbx_num_res / _struct_site_gen.site_id
Revision 2.1Nov 20, 2019Group: Advisory / Derived calculations
Category: pdbx_struct_conn_angle / pdbx_validate_close_contact / struct_conn
Revision 3.0Apr 9, 2025Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Non-polymer description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / pdbx_validate_chiral / struct_conn / struct_conn_type
Item: _chem_comp.formula / _chem_comp.pdbx_synonyms ..._chem_comp.formula / _chem_comp.pdbx_synonyms / _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.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_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_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_type.id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Photosystem I P700 chlorophyll a apoprotein A1
B: Photosystem I P700 chlorophyll a apoprotein A2
C: Photosystem I iron-sulfur center
D: Photosystem I reaction center subunit II
E: Photosystem I reaction center subunit IV
F: Photosystem I reaction center subunit III
I: Photosystem I reaction center subunit VIII
J: Photosystem I reaction center subunit IX
K: Photosystem I reaction center subunit PsaK 2
L: Photosystem I reaction center subunit XI
M: Photosystem I reaction center subunit XII
a: Photosystem I P700 chlorophyll a apoprotein A1
b: Photosystem I P700 chlorophyll a apoprotein A2
c: Photosystem I iron-sulfur center
d: Photosystem I reaction center subunit II
e: Photosystem I reaction center subunit IV
f: Photosystem I reaction center subunit III
i: Photosystem I reaction center subunit VIII
j: Photosystem I reaction center subunit IX
k: Photosystem I reaction center subunit PsaK 2
l: Photosystem I reaction center subunit XI
m: Photosystem I reaction center subunit XII
1: Photosystem I P700 chlorophyll a apoprotein A1
2: Photosystem I P700 chlorophyll a apoprotein A2
3: Photosystem I iron-sulfur center
4: Photosystem I reaction center subunit II
5: Photosystem I reaction center subunit IV
6: Photosystem I reaction center subunit III
h: Photosystem I reaction center subunit VIII
7: Photosystem I reaction center subunit IX
8: Photosystem I reaction center subunit PsaK 2
0: Photosystem I reaction center subunit XI
9: Photosystem I reaction center subunit XII
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,087,723476
Polymers746,42833
Non-polymers341,294443
Water16,015889
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)212.170, 137.622, 225.095
Angle α, β, γ (deg.)90.00, 116.74, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Photosystem I P700 chlorophyll a apoprotein ... , 4 types, 6 molecules AaB2b1

#1: Protein Photosystem I P700 chlorophyll a apoprotein A1 / PsaA


Mass: 83036.398 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Synechocystis sp. PCC 6803 (bacteria) / References: UniProt: P29254, photosystem I
#2: Protein Photosystem I P700 chlorophyll a apoprotein A2 / PsaB


Mass: 81369.531 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Synechocystis sp. PCC 6803 (bacteria) / References: UniProt: P29255, photosystem I
#12: Protein Photosystem I P700 chlorophyll a apoprotein A2 / PsaB


Mass: 81167.258 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Synechocystis sp. PCC 6803 (bacteria) / References: UniProt: P29255, photosystem I
#16: Protein Photosystem I P700 chlorophyll a apoprotein A1 / PsaA


Mass: 82280.516 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Synechocystis sp. PCC 6803 (bacteria) / References: UniProt: P29254, photosystem I

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Photosystem I iron-sulfur ... , 2 types, 3 molecules C3c

#3: Protein Photosystem I iron-sulfur center / 9 kDa polypeptide / PSI-C / Photosystem I subunit VII / PsaC


Mass: 8706.064 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Synechocystis sp. PCC 6803 (bacteria) / References: UniProt: P32422, photosystem I
#13: Protein Photosystem I iron-sulfur center / 9 kDa polypeptide / PSI-C / Photosystem I subunit VII / PsaC


Mass: 8837.261 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Synechocystis sp. PCC 6803 (bacteria) / References: UniProt: P32422, photosystem I

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Photosystem I reaction center subunit ... , 14 types, 24 molecules DdE5Ff6IiJj7KLlMm9ek4h80

#4: Protein Photosystem I reaction center subunit II / Photosystem I 16 kDa polypeptide / PSI-D


Mass: 15663.749 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Synechocystis sp. PCC 6803 (bacteria) / References: UniProt: P19569
#5: Protein Photosystem I reaction center subunit IV / Photosystem I 8.1 kDa protein / p30 protein


Mass: 7680.478 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Synechocystis sp. PCC 6803 (bacteria) / References: UniProt: P12975
#6: Protein Photosystem I reaction center subunit III / PSI-F


Mass: 15791.086 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Synechocystis sp. PCC 6803 (bacteria) / References: UniProt: P29256
#7: Protein/peptide Photosystem I reaction center subunit VIII


Mass: 4414.148 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Synechocystis sp. PCC 6803 (bacteria) / References: UniProt: Q55330
#8: Protein/peptide Photosystem I reaction center subunit IX


Mass: 4535.415 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Synechocystis sp. PCC 6803 (bacteria) / References: UniProt: Q55329
#9: Protein Photosystem I reaction center subunit PsaK 2 / Photosystem I subunit X 2


Mass: 8237.783 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Synechocystis sp. PCC 6803 (bacteria) / References: UniProt: P74564
#10: Protein Photosystem I reaction center subunit XI / PSI subunit V / PSI-L


Mass: 16631.795 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Synechocystis sp. PCC 6803 (bacteria) / References: UniProt: P37277
#11: Protein/peptide Photosystem I reaction center subunit XII / PSI-M


Mass: 3382.063 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Synechocystis sp. PCC 6803 (bacteria) / References: UniProt: P72986
#14: Protein Photosystem I reaction center subunit IV / Photosystem I 8.1 kDa protein / p30 protein


Mass: 7552.350 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Synechocystis sp. PCC 6803 (bacteria) / References: UniProt: P12975
#15: Protein Photosystem I reaction center subunit PsaK 2 / Photosystem I subunit X 2


Mass: 8037.548 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Synechocystis sp. PCC 6803 (bacteria) / References: UniProt: P74564
#17: Protein Photosystem I reaction center subunit II / Photosystem I 16 kDa polypeptide / PSI-D


Mass: 15532.552 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Synechocystis sp. PCC 6803 (bacteria) / References: UniProt: P19569
#18: Protein/peptide Photosystem I reaction center subunit VIII


Mass: 4227.982 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Synechocystis sp. PCC 6803 (bacteria) / References: UniProt: Q55330
#19: Protein Photosystem I reaction center subunit PsaK 2 / Photosystem I subunit X 2


Mass: 8124.626 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Synechocystis sp. PCC 6803 (bacteria) / References: UniProt: P74564
#20: Protein Photosystem I reaction center subunit XI / PSI subunit V / PSI-L


Mass: 16300.407 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Synechocystis sp. PCC 6803 (bacteria) / References: UniProt: P37277

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Sugars , 2 types, 6 molecules

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


Type: D-saccharide / Mass: 510.615 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C24H46O11 / Comment: detergent*YM
#37: Sugar ChemComp-DGD / DIGALACTOSYL DIACYL GLYCEROL (DGDG)


Type: saccharide / Mass: 949.299 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C51H96O15

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Non-polymers , 16 types, 1326 molecules

#21: Chemical...
ChemComp-CLA / CHLOROPHYLL A


Mass: 893.489 Da / Num. of mol.: 285 / Source method: obtained synthetically / Formula: C55H72MgN4O5
#22: Chemical
ChemComp-PQN / PHYLLOQUINONE / VITAMIN K1 / 2-METHYL-3-PHYTYL-1,4-NAPHTHOQUINONE


Mass: 450.696 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C31H46O2
#23: Chemical
ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Fe4S4
#24: Chemical...
ChemComp-BCR / BETA-CAROTENE


Mass: 536.873 Da / Num. of mol.: 58 / Source method: obtained synthetically / Formula: C40H56
#25: Chemical...
ChemComp-LHG / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE


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


Mass: 787.158 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C45H86O10
#27: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H3O2
#28: Chemical ChemComp-45D / beta,beta-carotene-4,4'-dione / Isomer of Canthaxanthin


Mass: 564.840 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C40H52O2
#29: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#30: Chemical
ChemComp-ECH / beta,beta-caroten-4-one / echinenone


Mass: 550.856 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C40H54O
#31: 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.: 7 / Source method: obtained synthetically / Formula: C41H78O12S
#32: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Ca
#33: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#34: Chemical
ChemComp-ZEX / (1R,2S)-4-{(1E,3E,5E,7E,9E,11E,13E,15E,17E)-18-[(4S)-4-hydroxy-2,6,6-trimethylcyclohex-1-en-1-yl]-3,7,12,16-tetramethyloctadeca-1,3,5,7,9,11,13,15,17-nonaen-1-yl}-2,5,5-trimethylcyclohex-3-en-1-ol


Mass: 568.871 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C40H56O2
#36: Chemical ChemComp-EQ3 / (3'R)-3'-hydroxy-beta,beta-caroten-4-one / 3'-Hydroxyechinenone / 3'-OH-Echinenone


Mass: 566.856 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C40H54O2
#38: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 889 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.22 Å3/Da / Density % sol: 44.65 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: PEG 3350, magnesium chloride, tricine, glycine, magnesium acetate

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.999 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Mar 18, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.999 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 395994 / % possible obs: 99.8 % / Redundancy: 23.3 % / Rmerge(I) obs: 0.078 / Net I/σ(I): 7.6
Reflection shellResolution: 2.5→2.54 Å / Redundancy: 21.8 % / Mean I/σ(I) obs: 0.5 / % possible all: 98.4

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Processing

Software
NameVersionClassification
PHENIX(dev_2947: ???)refinement
XDSdata reduction
Aimlessdata reduction
XSCALEdata scaling
MOLREPphasing
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 2.501→49.481 Å / SU ML: 0.44 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 31.11 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2644 7881 1.99 %
Rwork0.2276 --
obs0.2283 395994 99.44 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.501→49.481 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms52782 0 23440 889 77111
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00580232
X-RAY DIFFRACTIONf_angle_d1.412112844
X-RAY DIFFRACTIONf_dihedral_angle_d25.83332578
X-RAY DIFFRACTIONf_chiral_restr0.0639961
X-RAY DIFFRACTIONf_plane_restr0.01813267
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5008-2.52920.38822650.356912420X-RAY DIFFRACTION96
2.5292-2.5590.3562500.342412724X-RAY DIFFRACTION98
2.559-2.59020.37332800.34412773X-RAY DIFFRACTION99
2.5902-2.6230.35812730.340212791X-RAY DIFFRACTION99
2.623-2.65750.41682690.345112866X-RAY DIFFRACTION99
2.6575-2.69390.34432640.337812928X-RAY DIFFRACTION100
2.6939-2.73240.37012670.326112840X-RAY DIFFRACTION100
2.7324-2.77320.34572680.317512904X-RAY DIFFRACTION100
2.7732-2.81650.36692570.313212959X-RAY DIFFRACTION100
2.8165-2.86270.33442650.305912924X-RAY DIFFRACTION100
2.8627-2.9120.34162350.301812996X-RAY DIFFRACTION100
2.912-2.9650.34032600.294812905X-RAY DIFFRACTION100
2.965-3.0220.35872630.292512927X-RAY DIFFRACTION100
3.022-3.08370.31022310.282813012X-RAY DIFFRACTION100
3.0837-3.15070.30652510.27112967X-RAY DIFFRACTION100
3.1507-3.2240.30332920.268512933X-RAY DIFFRACTION100
3.224-3.30460.28373050.255212893X-RAY DIFFRACTION100
3.3046-3.39390.31212910.251312916X-RAY DIFFRACTION100
3.3939-3.49380.29552820.245112894X-RAY DIFFRACTION100
3.4938-3.60650.27732650.226813009X-RAY DIFFRACTION100
3.6065-3.73530.26022810.221312909X-RAY DIFFRACTION100
3.7353-3.88480.24632830.210512927X-RAY DIFFRACTION100
3.8848-4.06160.24342650.200912929X-RAY DIFFRACTION99
4.0616-4.27560.21632610.185612964X-RAY DIFFRACTION100
4.2756-4.54330.22312770.179712982X-RAY DIFFRACTION100
4.5433-4.89380.19652590.175213046X-RAY DIFFRACTION100
4.8938-5.38580.24872670.181813034X-RAY DIFFRACTION100
5.3858-6.16380.2182320.195513102X-RAY DIFFRACTION100
6.1638-7.76090.18122140.177513221X-RAY DIFFRACTION100
7.7609-49.4910.24612090.216813418X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.6282-0.08450.05410.77830.0340.3878-0.02730.2062-0.0354-0.2605-0.0242-0.06150.03350.0832-0.02530.43580.00530.09860.33720.00990.3894139.2278-67.7845-20.5694
20.7677-0.1323-0.15950.7380.17080.5777-0.042-0.51880.03860.51880.01640.0540.15510.1346-0.00160.9709-0.02910.03390.8005-0.0790.3312111.7975-70.186566.6228
30.6268-0.0403-0.00510.66440.00890.6388-0.0099-0.5776-0.3060.56310.0723-0.48740.11940.29330.35170.980.204-0.35891.01160.30890.8826194.5401-84.857759.0757
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain 'A' and resid 1 through 5004) or (chain 'B' and resid 1 through 5005) or (chain 'C' and resid 2 through 3003) or (chain 'D' and resid 1 through 141) or (chain 'E' and resid 1 through 70) or (chain 'F' and resid 1 through 4016) or (chain 'I' and resid 1 through 4020) or (chain 'J' and resid 1 through 4013) or (chain 'K' and resid 9 through 1402) or (chain 'L' and resid 1 through 6001) or (chain 'M' and resid 1 through 4021)
2X-RAY DIFFRACTION2(chain 'a' and resid 1 through 5004) or (chain 'b' and resid 3 through 5006) or (chain 'c' and resid 2 through 3003) or (chain 'd' and resid 1 through 141) or (chain 'e' and resid 1 through 69) or (chain 'f' and resid 1 through 4016) or (chain 'i' and resid 1 through 4020) or (chain 'j' and resid 1 through 4013) or (chain 'k' and resid 9 through 4001) or (chain 'l' and resid 1 through 5003) or (chain 'm' and resid 1 through 4021)
3X-RAY DIFFRACTION3(chain '1' and resid 1 through 5004) or (chain '2' and resid 4 through 5005) or (chain '3' and resid 2 through 3003) or (chain '4' and resid 1 through 141) or (chain '5' and resid 1 through 74) or (chain '6' and resid 1 through 4016) or (chain 'h' and resid 1 through 4020) or (chain '7' and resid 1 through 4013) or (chain '8' and resid 9 through 4001) or (chain '0' and resid 4 through 6001) or (chain '9' and resid 1 through 4021)

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