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- PDB-2wsc: Improved Model of Plant Photosystem I -

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Basic information

Entry
Database: PDB / ID: 2wsc
TitleImproved Model of Plant Photosystem I
Components
  • (PHOTOSYSTEM I P700 CHLOROPHYLL A APOPROTEIN ...) x 2
  • (PHOTOSYSTEM I REACTION CENTER SUBUNIT ...) x 9
  • (PHOTOSYSTEM I-N ...) x 2
  • AT3G54890
  • CHLOROPHYLL A-B BINDING PROTEIN P4, CHLOROPLASTIC
  • LHCA3
  • PHOTOSYSTEM I IRON-SULFUR CENTER
  • TYPE II CHLOROPHYLL A/B BINDING PROTEIN FROM PHOTOSYSTEM I
KeywordsPHOTOSYNTHESIS / ELECTRON TRANSFER / MEMBRANE PROTEINS / LARGE COMPLEXES
Function / homology
Function and homology information


chloroplast photosystem I / response to low light intensity stimulus / plastoglobule / response to high light intensity / chloroplast thylakoid / photosynthesis, light harvesting in photosystem I / thylakoid / photosynthesis, light harvesting / chloroplast thylakoid lumen / chloroplast envelope ...chloroplast photosystem I / response to low light intensity stimulus / plastoglobule / response to high light intensity / chloroplast thylakoid / photosynthesis, light harvesting in photosystem I / thylakoid / photosynthesis, light harvesting / chloroplast thylakoid lumen / chloroplast envelope / photosystem I reaction center / photosystem I / photosynthetic electron transport in photosystem I / photosystem I / photosystem II / chlorophyll binding / chloroplast thylakoid membrane / photosynthesis / response to cold / chloroplast / phosphoprotein binding / 4 iron, 4 sulfur cluster binding / molecular adaptor activity / oxidoreductase activity / electron transfer activity / protein domain specific binding / mRNA binding / magnesium ion binding / metal ion binding / plasma membrane
Similarity search - Function
Chlorophyll A-B binding protein fold / Chlorophyll A-B binding protein / Chlorophyll a-b binding protein like / Photosystem I reaction centre subunit N, chloroplastic / Photosystem I reaction centre subunit N superfamily / Photosystem I reaction centre subunit N (PSAN or PSI-N) / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #220 / Photosystem I, reaction centre, subunit PsaF / Photosystem I p700 chlorophyll A apoprotein A1 / Photosystem I PsaA/PsaB ...Chlorophyll A-B binding protein fold / Chlorophyll A-B binding protein / Chlorophyll a-b binding protein like / Photosystem I reaction centre subunit N, chloroplastic / Photosystem I reaction centre subunit N superfamily / Photosystem I reaction centre subunit N (PSAN or PSI-N) / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #220 / 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 / GTP Cyclohydrolase I; Chain A, domain 1 / Photosystem 1 Reaction Centre Subunit Xi; Chain: L; / Photosystem I PsaL, reaction centre subunit XI / Single helix bin / Photosystem I PsaH, reaction centre subunit VI / Photosystem I reaction centre subunit VI / Photosystem I reaction center subunit V / 4Fe-4S dicluster domain / Photosystem I reaction center subunit psaK, plant / Photosystem I reaction center subunit V/PsaK, plant / Photosystem I PsaG/PsaK domain, chloroplastic / SH3 type barrels. - #50 / 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 / Alpha-Beta Plaits - #20 / 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 / 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 / Chlorophyll A-B binding protein, plant and chromista / Photosystem I PsaJ, reaction centre subunit IX / Photosystem I reaction centre subunit IX / PsaJ / Chlorophyll A-B binding protein / Chlorophyll A-B binding protein / Photosystem I protein PsaC / Photosystem I PsaA / Photosystem I PsaB / 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 / 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. / Few Secondary Structures / Irregular / Roll / Alpha-Beta Plaits / Up-down Bundle / 2-Layer Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
sucrose / BETA-CAROTENE / CHLOROPHYLL A / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / PHYLLOQUINONE / IRON/SULFUR CLUSTER / Unknown ligand / Chlorophyll a-b binding protein, chloroplastic / Photosystem I P700 chlorophyll a apoprotein A1 / Photosystem I P700 chlorophyll a apoprotein A2 ...sucrose / BETA-CAROTENE / CHLOROPHYLL A / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / PHYLLOQUINONE / IRON/SULFUR CLUSTER / Unknown ligand / Chlorophyll a-b binding protein, chloroplastic / Photosystem I P700 chlorophyll a apoprotein A1 / Photosystem I P700 chlorophyll a apoprotein A2 / Photosystem I iron-sulfur center / Photosystem I reaction center subunit II, chloroplastic / Photosystem I reaction center subunit III, chloroplastic / Photosystem I reaction center subunit V, chloroplastic / Photosystem I reaction center subunit VIII / Photosystem I reaction center subunit IX / Photosystem I reaction center subunit VI, chloroplastic / Photosystem I reaction center subunit psaK, chloroplastic / Chlorophyll a-b binding protein 6, chloroplastic / Chlorophyll a-b binding protein, chloroplastic / Photosystem I reaction center subunit XI, chloroplastic / Photosystem I reaction center subunit N, chloroplastic / Chlorophyll a-b binding protein 6, chloroplastic / Photosystem I reaction center subunit IV A, chloroplastic / Chlorophyll a-b binding protein P4, chloroplastic
Similarity search - Component
Biological speciesARABIDOPSIS THALIANA (thale cress)
PISUM SATIVUM (garden pea)
GLYCINE MAX (soybean)
SPINACIA OLERACEA (spinach)
HORDEUM VULGARE (barley)
PHASEOLUS VULGARIS (common bean)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 Å
AuthorsAmunts, A. / Toporik, H. / Borovikov, A. / Nelson, N.
CitationJournal: J.Biol.Chem. / Year: 2010
Title: Structure Determination and Improved Model of Plant Photosystem I.
Authors: Amunts, A. / Toporik, H. / Borovikova, A. / Nelson, N.
History
DepositionSep 4, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 17, 2009Provider: repository / Type: Initial release
Revision 1.1Aug 8, 2012Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Non-polymer description / Other / Structure summary / Version format compliance
Revision 1.2Jun 20, 2018Group: Advisory / Data collection / Derived calculations
Category: database_PDB_caveat / pdbx_struct_conn_angle ...database_PDB_caveat / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_close_contact / pdbx_validate_symm_contact / struct_conn
Revision 1.3Oct 24, 2018Group: Advisory / Data collection / Derived calculations
Category: pdbx_validate_close_contact / pdbx_validate_symm_contact / struct_conn
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Non-polymer description / Other / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_PDB_caveat / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / 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_conn_type / 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.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 / _database_PDB_caveat.text / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.src_method / _entity.type / _pdbx_database_status.status_code_sf / _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.value / _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 / _pdbx_validate_chiral.auth_asym_id / _pdbx_validate_chiral.auth_atom_id / _pdbx_validate_chiral.auth_comp_id / _pdbx_validate_chiral.auth_seq_id / _pdbx_validate_chiral.details / _struct_asym.entity_id / _struct_conn_type.id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
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_validate_chiral / struct_conn
Item: _chem_comp.formula / _chem_comp.pdbx_synonyms ..._chem_comp.formula / _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag
Revision 4.0Oct 1, 2025Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / entity ...atom_site / entity / pdbx_entity_nonpoly / pdbx_modification_feature / pdbx_nonpoly_scheme / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_chiral / pdbx_validate_close_contact / pdbx_validate_symm_contact / struct_asym / struct_conn
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.type_symbol / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _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_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.value / _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 / _pdbx_validate_chiral.auth_asym_id / _pdbx_validate_chiral.auth_atom_id / _pdbx_validate_chiral.auth_comp_id / _pdbx_validate_chiral.auth_seq_id / _pdbx_validate_chiral.details / _pdbx_validate_symm_contact.auth_seq_id_1 / _pdbx_validate_symm_contact.auth_seq_id_2 / _struct_asym.entity_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
1: AT3G54890
2: TYPE II CHLOROPHYLL A/B BINDING PROTEIN FROM PHOTOSYSTEM I
3: LHCA3
4: CHLOROPHYLL A-B BINDING PROTEIN P4, CHLOROPLASTIC
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, CHLOROPLASTIC
E: PHOTOSYSTEM I REACTION CENTER SUBUNIT IV A, CHLOROPLASTIC
F: PHOTOSYSTEM I REACTION CENTER SUBUNIT III, CHLOROPLASTIC
G: PHOTOSYSTEM I REACTION CENTER SUBUNIT V, CHLOROPLASTIC
H: PHOTOSYSTEM I REACTION CENTER SUBUNIT VI, CHLOROPLASTIC
I: PHOTOSYSTEM I REACTION CENTER SUBUNIT VIII
J: PHOTOSYSTEM I REACTION CENTER SUBUNIT IX
K: PHOTOSYSTEM I REACTION CENTER SUBUNIT PSAK, CHLOROPLASTIC
L: PHOTOSYSTEM I REACTION CENTER SUBUNIT XI, CHLOROPLASTIC
N: PHOTOSYSTEM I-N SUBUNIT
R: PHOTOSYSTEM I-N SUBUNIT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)648,578274
Polymers454,17018
Non-polymers194,408256
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)120.655, 189.086, 129.388
Angle α, β, γ (deg.)90.00, 91.24, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 5 types, 5 molecules 1234C

#1: Protein AT3G54890 / LHCA1


Mass: 26021.895 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ARABIDOPSIS THALIANA (thale cress) / References: UniProt: Q9C5R7, UniProt: Q01667*PLUS
#2: Protein TYPE II CHLOROPHYLL A/B BINDING PROTEIN FROM PHOTOSYSTEM I / LHCA2


Mass: 28926.746 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) PISUM SATIVUM (garden pea) / References: UniProt: Q41038
#3: Protein LHCA3


Mass: 29852.055 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) GLYCINE MAX (soybean) / References: UniProt: C6TEX2*PLUS
#4: Protein CHLOROPHYLL A-B BINDING PROTEIN P4, CHLOROPLASTIC / LHCI TYPE III CAB-P4 LHCA4


Mass: 27181.982 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) PISUM SATIVUM (garden pea) / References: UniProt: Q9SQL2
#7: Protein PHOTOSYSTEM I IRON-SULFUR CENTER / PSAC / PHOTOSYSTEM I SUBUNIT VII / 9 KDA POLYPEPTIDE / PSI-C


Mass: 8991.474 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) PISUM SATIVUM (garden pea) / References: UniProt: P10793

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PHOTOSYSTEM I P700 CHLOROPHYLL A APOPROTEIN ... , 2 types, 2 molecules AB

#5: Protein PHOTOSYSTEM I P700 CHLOROPHYLL A APOPROTEIN A1 / PSAA / PSI-A


Mass: 84284.516 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) PISUM SATIVUM (garden pea) / References: UniProt: P05310
#6: Protein PHOTOSYSTEM I P700 CHLOROPHYLL A APOPROTEIN A2 / PSAB / PSI-B


Mass: 82490.961 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) PISUM SATIVUM (garden pea) / References: UniProt: P05311

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PHOTOSYSTEM I REACTION CENTER SUBUNIT ... , 9 types, 9 molecules DEFGHIJKL

#8: Protein PHOTOSYSTEM I REACTION CENTER SUBUNIT II, CHLOROPLASTIC / PSAD / PHOTOSYSTEM I 20 KDA SUBUNIT / PSI-D


Mass: 23170.641 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SPINACIA OLERACEA (spinach) / References: UniProt: P12353
#9: Protein PHOTOSYSTEM I REACTION CENTER SUBUNIT IV A, CHLOROPLASTIC / PSAE / PSI-E A


Mass: 14984.955 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ARABIDOPSIS THALIANA (thale cress) / References: UniProt: Q9S831
#10: Protein PHOTOSYSTEM I REACTION CENTER SUBUNIT III, CHLOROPLASTIC / PSAF / LIGHT-HARVESTING COMPLEX I 17 KDA PROTEIN / PSI-F


Mass: 25445.453 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SPINACIA OLERACEA (spinach) / References: UniProt: P12355
#11: Protein PHOTOSYSTEM I REACTION CENTER SUBUNIT V, CHLOROPLASTIC / PSAG / PSI-G / PHOTOSYSTEM I 9 KDA PROTEIN


Mass: 18232.650 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SPINACIA OLERACEA (spinach) / References: UniProt: P12357
#12: Protein PHOTOSYSTEM I REACTION CENTER SUBUNIT VI, CHLOROPLASTIC / PSAH / PSI-H / LIGHT-HARVESTING COMPLEX I 11 KDA PROTEIN


Mass: 15341.604 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SPINACIA OLERACEA (spinach) / References: UniProt: P22179
#13: Protein/peptide PHOTOSYSTEM I REACTION CENTER SUBUNIT VIII / PSAI / PSI-I


Mass: 4474.527 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) PISUM SATIVUM (garden pea) / References: UniProt: P17227
#14: Protein/peptide PHOTOSYSTEM I REACTION CENTER SUBUNIT IX / PSAJ / PSI-J


Mass: 5079.930 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SPINACIA OLERACEA (spinach) / References: UniProt: P17230
#15: Protein PHOTOSYSTEM I REACTION CENTER SUBUNIT PSAK, CHLOROPLASTIC / PSAK / PHOTOSYSTEM I SUBUNIT X / PSI-K / LIGHT-HARVESTING COMPLEX I 7 KDA PROTEIN


Mass: 13742.934 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) HORDEUM VULGARE (barley) / References: UniProt: P36886
#16: Protein PHOTOSYSTEM I REACTION CENTER SUBUNIT XI, CHLOROPLASTIC / PSAL / PSI-L / PSI SUBUNIT V


Mass: 22957.676 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SPINACIA OLERACEA (spinach) / References: UniProt: Q41385

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PHOTOSYSTEM I-N ... , 2 types, 2 molecules NR

#17: Protein PHOTOSYSTEM I-N SUBUNIT / PSAN / PSI-N


Mass: 18460.988 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) PHASEOLUS VULGARIS (common bean) / References: UniProt: Q84U30
#18: Protein PHOTOSYSTEM I-N SUBUNIT


Mass: 4528.573 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) PISUM SATIVUM (garden pea)

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Sugars , 2 types, 58 molecules

#19: Polysaccharide
beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose / sucrose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 13
Source method: isolated from a genetically manipulated source
Details: oligosaccharide with reducing-end-to-reducing-end glycosidic bond
References: sucrose
DescriptorTypeProgram
DFrufb2-1DGlcpaGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[ha122h-2b_2-5][a2122h-1a_1-5]/1-2/a2-b1WURCSPDB2Glycan 1.1.0
[][a-D-Fruf]{y-Glcp]{[(2+1)][a-D-6-deoxy-Glcp]{}}LINUCSPDB-CARE
#21: Sugar...
ChemComp-LMU / DODECYL-ALPHA-D-MALTOSIDE


Type: D-saccharide / Mass: 510.615 Da / Num. of mol.: 45 / Source method: obtained synthetically / Formula: C24H46O11 / Comment: detergent*YM

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Non-polymers , 6 types, 198 molecules

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


Mass: 893.489 Da / Num. of mol.: 173 / Source method: obtained synthetically / Formula: C55H72MgN4O5
#22: Chemical
ChemComp-BCR / BETA-CAROTENE


Mass: 536.873 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: C40H56
#23: Chemical ChemComp-PQN / PHYLLOQUINONE / VITAMIN K1 / 2-METHYL-3-PHYTYL-1,4-NAPHTHOQUINONE


Mass: 450.696 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C31H46O2
#24: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Fe4S4
#25: Chemical ChemComp-LMG / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE


Mass: 787.158 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C45H86O10
#26: Chemical ChemComp-UNL / UNKNOWN LIGAND


Num. of mol.: 1 / Source method: obtained synthetically

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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: 2.3 Å3/Da / Density % sol: 44 % / Description: NONE
Crystal growpH: 6
Details: 22.5 MM MES BIS-TRIS PH 6 10MM SUCCINIC ACID 6% PEG6000 0.015% DTM

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.873
DetectorType: MARRESEARCH / Detector: CCD / Date: Mar 12, 2009 / Details: MIRRORS
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.873 Å / Relative weight: 1
ReflectionResolution: 3.3→50 Å / Num. obs: 88964 / % possible obs: 99 % / Observed criterion σ(I): 2 / Redundancy: 4.3 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 17.2
Reflection shellResolution: 3.3→3.43 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 2.8 / % possible all: 95.2

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Processing

Software
NameVersionClassification
REFMAC5.5.0072refinement
DENZOdata reduction
SCALEPACKdata scaling
MRphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1YO9

1yo9


Resolution: 3.3→30 Å / Cor.coef. Fo:Fc: 0.771 / Cor.coef. Fo:Fc free: 0.762 / SU B: 0.001 / SU ML: 0 / Cross valid method: THROUGHOUT / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.36594 4344 5 %RANDOM
Rwork0.36253 ---
obs0.3627 82166 99.46 %-
Solvent computationSolvent model: NONE
Displacement parametersBiso mean: 23.117 Å2
Baniso -1Baniso -2Baniso -3
1--1.8 Å20 Å2-1.51 Å2
2---7.93 Å20 Å2
3---9.67 Å2
Refinement stepCycle: LAST / Resolution: 3.3→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms24841 0 11538 0 36379
LS refinement shellResolution: 3.3→3.385 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.48 276 -
Rwork0.522 5893 -
obs--97.44 %

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