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- PDB-4xk8: Crystal structure of plant photosystem I-LHCI super-complex at 2.... -

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Basic information

Entry
Database: PDB / ID: 4xk8
TitleCrystal structure of plant photosystem I-LHCI super-complex at 2.8 angstrom resolution
Components
  • (Chlorophyll a-b binding protein ...) x 3
  • (Photosystem I P700 chlorophyll a apoprotein ...) x 2
  • (Photosystem I reaction center subunit ...) x 5
  • (Putative uncharacterized ...) x 3
  • Photosystem I iron-sulfur center
  • Type II chlorophyll a/b binding protein from photosystem I
  • Uncharacterized protein
KeywordsPHOTOSYNTHESIS / photosystem i / plant LHCI-PSI supercomplex
Function / homology
Function and homology information


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 ...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 / chloroplast / response to cold / phosphoprotein binding / 4 iron, 4 sulfur cluster binding / electron transfer activity / oxidoreductase activity / protein domain specific binding / mRNA binding / magnesium ion binding / metal ion binding
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 / Photosystem I PsaH, reaction centre subunit VI / Photosystem I reaction centre subunit VI / Photosystem I reaction center subunit V ...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 / 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 / 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 / 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 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 / 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 / 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-CAROTENE / CHLOROPHYLL B / CHLOROPHYLL A / DIGALACTOSYL DIACYL GLYCEROL (DGDG) / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / Chem-LUT / PHYLLOQUINONE / IRON/SULFUR CLUSTER / Chem-XAT ...BETA-CAROTENE / CHLOROPHYLL B / CHLOROPHYLL A / DIGALACTOSYL DIACYL GLYCEROL (DGDG) / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / Chem-LUT / PHYLLOQUINONE / IRON/SULFUR CLUSTER / Chem-XAT / Photosystem I reaction center subunit IX / Photosystem I reaction center subunit II, chloroplastic / Photosystem I reaction center subunit VI / Photosystem I reaction center subunit IV / Photosystem I reaction center subunit XI, chloroplastic / Photosystem I reaction center subunit psaK, chloroplastic / Photosystem I reaction center subunit II, 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 III, chloroplastic / Photosystem I reaction center subunit V, chloroplastic / Photosystem I reaction center subunit VIII / Chlorophyll a-b binding protein 6, chloroplastic / Chlorophyll a-b binding protein 3, chloroplastic / Chlorophyll a-b binding protein, chloroplastic / Chlorophyll a-b binding protein P4, chloroplastic
Similarity search - Component
Biological speciesPisum sativum (garden pea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.8 Å
AuthorsSuga, M. / Qin, X. / Kuang, T. / Shen, J.R.
CitationJournal: Science / Year: 2015
Title: Photosynthesis. Structural basis for energy transfer pathways in the plant PSI-LHCI supercomplex.
Authors: Xiaochun Qin / Michihiro Suga / Tingyun Kuang / Jian-Ren Shen /
Abstract: Photosynthesis converts solar energy to chemical energy by means of two large pigment-protein complexes: photosystem I (PSI) and photosystem II (PSII). In higher plants, the PSI core is surrounded by ...Photosynthesis converts solar energy to chemical energy by means of two large pigment-protein complexes: photosystem I (PSI) and photosystem II (PSII). In higher plants, the PSI core is surrounded by a large light-harvesting complex I (LHCI) that captures sunlight and transfers the excitation energy to the core with extremely high efficiency. We report the structure of PSI-LHCI, a 600-kilodalton membrane protein supercomplex, from Pisum sativum (pea) at a resolution of 2.8 angstroms. The structure reveals the detailed arrangement of pigments and other cofactors—especially within LHCI—as well as numerous specific interactions between the PSI core and LHCI. These results provide a firm structural basis for our understanding on the energy transfer and photoprotection mechanisms within the PSI-LHCI supercomplex.
History
DepositionJan 10, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 10, 2015Provider: repository / Type: Initial release
Revision 1.1Jul 8, 2015Group: Derived calculations
Revision 1.2May 1, 2019Group: Advisory / Data collection ...Advisory / Data collection / Derived calculations / Source and taxonomy
Category: database_PDB_caveat / diffrn_source ...database_PDB_caveat / diffrn_source / entity_src_nat / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_oper_list / pdbx_validate_chiral
Item: _diffrn_source.pdbx_synchrotron_site / _entity_src_nat.pdbx_alt_source_flag ..._diffrn_source.pdbx_synchrotron_site / _entity_src_nat.pdbx_alt_source_flag / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Mar 4, 2020Group: Source and taxonomy / Structure summary / Category: entity / entity_src_nat / pdbx_entity_src_syn / Item: _entity.src_method
Revision 1.4Jul 29, 2020Group: Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.pdbx_synonyms ..._chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _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 / _struct_conn.pdbx_dist_value / _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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.0Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / 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
Item: _chem_comp.formula / _chem_comp.pdbx_synonyms ..._chem_comp.formula / _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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: Uncharacterized protein
E: Putative uncharacterized protein
F: Photosystem I reaction center subunit III, chloroplastic
G: Photosystem I reaction center subunit V, chloroplastic
H: Putative uncharacterized protein
I: Photosystem I reaction center subunit VIII
J: Photosystem I reaction center subunit IX
K: Photosystem I reaction center subunit X psaK
L: Putative uncharacterized protein
1: Chlorophyll a-b binding protein 6, chloroplastic
2: Type II chlorophyll a/b binding protein from photosystem I
3: Chlorophyll a-b binding protein 3, chloroplastic
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: Uncharacterized protein
e: Putative uncharacterized protein
f: Photosystem I reaction center subunit III, chloroplastic
g: Photosystem I reaction center subunit V, chloroplastic
h: Putative uncharacterized protein
i: Photosystem I reaction center subunit VIII
j: Photosystem I reaction center subunit IX
k: Photosystem I reaction center subunit X psaK
l: Putative uncharacterized protein
6: Chlorophyll a-b binding protein 6, chloroplastic
7: Type II chlorophyll a/b binding protein from photosystem I
8: Chlorophyll a-b binding protein 3, chloroplastic
9: Chlorophyll a-b binding protein P4, chloroplastic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,046,379446
Polymers711,56532
Non-polymers334,814414
Water3,333185
1
A: Photosystem I P700 chlorophyll a apoprotein A1
B: Photosystem I P700 chlorophyll a apoprotein A2
C: Photosystem I iron-sulfur center
D: Uncharacterized protein
E: Putative uncharacterized protein
F: Photosystem I reaction center subunit III, chloroplastic
G: Photosystem I reaction center subunit V, chloroplastic
H: Putative uncharacterized protein
I: Photosystem I reaction center subunit VIII
J: Photosystem I reaction center subunit IX
K: Photosystem I reaction center subunit X psaK
L: Putative uncharacterized protein
1: Chlorophyll a-b binding protein 6, chloroplastic
2: Type II chlorophyll a/b binding protein from photosystem I
3: Chlorophyll a-b binding protein 3, chloroplastic
4: Chlorophyll a-b binding protein P4, chloroplastic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)524,646225
Polymers355,78316
Non-polymers168,864209
Water19811
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
a: Photosystem I P700 chlorophyll a apoprotein A1
b: Photosystem I P700 chlorophyll a apoprotein A2
c: Photosystem I iron-sulfur center
d: Uncharacterized protein
e: Putative uncharacterized protein
f: Photosystem I reaction center subunit III, chloroplastic
g: Photosystem I reaction center subunit V, chloroplastic
h: Putative uncharacterized protein
i: Photosystem I reaction center subunit VIII
j: Photosystem I reaction center subunit IX
k: Photosystem I reaction center subunit X psaK
l: Putative uncharacterized protein
6: Chlorophyll a-b binding protein 6, chloroplastic
7: Type II chlorophyll a/b binding protein from photosystem I
8: Chlorophyll a-b binding protein 3, chloroplastic
9: Chlorophyll a-b binding protein P4, chloroplastic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)521,732221
Polymers355,78316
Non-polymers165,950205
Water18010
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)165.624, 192.220, 175.089
Angle α, β, γ (deg.)90.00, 91.41, 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 ... , 2 types, 4 molecules AaBb

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


Mass: 82408.281 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Pisum sativum (garden pea) / References: UniProt: P05310*PLUS
#2: Protein Photosystem I P700 chlorophyll a apoprotein A2 / PSI-B / PsaB


Mass: 82466.820 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Pisum sativum (garden pea) / References: UniProt: P05311*PLUS

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Protein , 3 types, 6 molecules CcDd27

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


Mass: 8860.276 Da / Num. of mol.: 2 / Fragment: UNP residues 2-81 / Source method: obtained synthetically / Source: (synth.) Pisum sativum (garden pea) / References: UniProt: P10793, photosystem I
#4: Protein Uncharacterized protein


Mass: 15853.142 Da / Num. of mol.: 2 / Fragment: UNP residues 63-203 / Source method: obtained synthetically / Source: (synth.) Pisum sativum (garden pea) / References: UniProt: I1NGD2, UniProt: A5Z2K3*PLUS
#14: Protein Type II chlorophyll a/b binding protein from photosystem I


Mass: 22693.666 Da / Num. of mol.: 2 / Fragment: UNP residues 62-267 / Source method: obtained synthetically / Source: (synth.) Pisum sativum (garden pea) / References: UniProt: Q41038

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Putative uncharacterized ... , 3 types, 6 molecules EeHhLl

#5: Protein Putative uncharacterized protein


Mass: 7299.219 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Pisum sativum (garden pea) / References: UniProt: E1C9K6*PLUS
#8: Protein Putative uncharacterized protein


Mass: 9639.886 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Pisum sativum (garden pea) / References: UniProt: C6T221*PLUS
#12: Protein Putative uncharacterized protein


Mass: 16130.484 Da / Num. of mol.: 2 / Fragment: UNP residues 4-156 / Source method: obtained synthetically / Source: (synth.) Pisum sativum (garden pea) / References: UniProt: E1C9L1

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Photosystem I reaction center subunit ... , 5 types, 10 molecules FfGgIiJjKk

#6: Protein Photosystem I reaction center subunit III, chloroplastic / Light-harvesting complex I 17 kDa protein / PSI-F


Mass: 17009.771 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Pisum sativum (garden pea) / References: UniProt: P12355*PLUS
#7: Protein Photosystem I reaction center subunit V, chloroplastic / PSI-G / Photosystem I 9 kDa protein


Mass: 10460.736 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Pisum sativum (garden pea) / References: UniProt: P12357*PLUS
#9: Protein/peptide Photosystem I reaction center subunit VIII / PSI-I


Mass: 3296.041 Da / Num. of mol.: 2 / Fragment: UNP residues 2-31 / Source method: obtained synthetically / Source: (synth.) Pisum sativum (garden pea) / References: UniProt: P17227
#10: Protein/peptide Photosystem I reaction center subunit IX / PSI-J


Mass: 4402.227 Da / Num. of mol.: 2 / Fragment: UNP residues 1-39 / Source method: obtained synthetically / Source: (synth.) Pisum sativum (garden pea) / References: UniProt: A4GGC6
#11: Protein Photosystem I reaction center subunit X psaK


Mass: 8462.847 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Pisum sativum (garden pea) / References: UniProt: E1C9L3

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Chlorophyll a-b binding protein ... , 3 types, 6 molecules 163849

#13: Protein Chlorophyll a-b binding protein 6, chloroplastic / LHCI-730 / LHCII type III CAB-6 / Light-harvesting complex protein Lhca1


Mass: 21354.418 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Pisum sativum (garden pea) / References: UniProt: Q01667*PLUS
#15: Protein Chlorophyll a-b binding protein 3, chloroplastic / LHCII type III CAB-3


Mass: 23725.020 Da / Num. of mol.: 2 / Fragment: UNP residues 55-272 / Source method: obtained synthetically / Source: (synth.) Pisum sativum (garden pea) / References: UniProt: Q32904
#16: Protein Chlorophyll a-b binding protein P4, chloroplastic / LHCI type III CAB-P4


Mass: 21719.670 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Pisum sativum (garden pea) / References: UniProt: Q9SQL2*PLUS

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Sugars , 3 types, 9 molecules

#22: Sugar
ChemComp-HTG / heptyl 1-thio-beta-D-glucopyranoside / HEPTYL 1-THIOHEXOPYRANOSIDE / heptyl 1-thio-beta-D-glucoside / heptyl 1-thio-D-glucoside / heptyl 1-thio-glucoside


Type: D-saccharide / Mass: 294.408 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C13H26O5S / Comment: detergent*YM
#23: Sugar ChemComp-LMT / DODECYL-BETA-D-MALTOSIDE


Type: D-saccharide / Mass: 510.615 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H46O11 / Comment: detergent*YM
#24: Sugar ChemComp-DGD / DIGALACTOSYL DIACYL GLYCEROL (DGDG)


Type: saccharide / Mass: 949.299 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C51H96O15

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Non-polymers , 10 types, 590 molecules

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


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


Mass: 450.696 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C31H46O2
#19: Chemical
ChemComp-LHG / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE


Mass: 722.970 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C38H75O10P / Comment: phospholipid*YM
#20: Chemical...
ChemComp-BCR / BETA-CAROTENE


Mass: 536.873 Da / Num. of mol.: 52 / Source method: obtained synthetically / Formula: C40H56
#21: Chemical
ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Fe4S4
#25: Chemical
ChemComp-LMG / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE


Mass: 787.158 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C45H86O10
#26: Chemical...
ChemComp-CHL / CHLOROPHYLL B


Mass: 907.472 Da / Num. of mol.: 24 / Source method: obtained synthetically / Formula: C55H70MgN4O6
#27: Chemical
ChemComp-LUT / (3R,3'R,6S)-4,5-DIDEHYDRO-5,6-DIHYDRO-BETA,BETA-CAROTENE-3,3'-DIOL / (3R,3'R)-BETA,BETA-CAROTENE-3,3'-DIOL / LUTEIN


Mass: 568.871 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C40H56O2
#28: Chemical
ChemComp-XAT / (3S,5R,6S,3'S,5'R,6'S)-5,6,5',6'-DIEPOXY-5,6,5',6'- TETRAHYDRO-BETA,BETA-CAROTENE-3,3'-DIOL / VIOLAXANTHIN


Mass: 600.870 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C40H56O4
#29: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 185 / 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

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Sample preparation

CrystalDensity Matthews: 3.92 Å3/Da / Density % sol: 68.59 %
Crystal growTemperature: 285 K / Method: vapor diffusion / Details: PEG

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 0.9 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Dec 11, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. obs: 268282 / % possible obs: 99.8 % / Redundancy: 7.5 % / Net I/σ(I): 7

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Processing

Software
NameVersionClassification
PHENIX1.8_1069refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementResolution: 2.8→49.147 Å / SU ML: 0.4 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.53 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2476 13498 5.03 %
Rwork0.2105 --
obs0.2123 268230 99.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.8→49.147 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms49678 0 21294 185 71157
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00675437
X-RAY DIFFRACTIONf_angle_d1.401106936
X-RAY DIFFRACTIONf_dihedral_angle_d21.45428690
X-RAY DIFFRACTIONf_chiral_restr0.0658954
X-RAY DIFFRACTIONf_plane_restr0.00412277
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8-2.83180.37014350.35148236X-RAY DIFFRACTION97
2.8318-2.86510.35094510.31478467X-RAY DIFFRACTION100
2.8651-2.90010.3274280.30398515X-RAY DIFFRACTION100
2.9001-2.93680.30914390.29838423X-RAY DIFFRACTION100
2.9368-2.97540.33864400.30978487X-RAY DIFFRACTION100
2.9754-3.01620.34764590.30298527X-RAY DIFFRACTION100
3.0162-3.05930.31814600.29068437X-RAY DIFFRACTION100
3.0593-3.10490.32844730.28368425X-RAY DIFFRACTION100
3.1049-3.15340.31534660.28058462X-RAY DIFFRACTION100
3.1534-3.20510.3144360.27618526X-RAY DIFFRACTION100
3.2051-3.26040.30754170.27378490X-RAY DIFFRACTION100
3.2604-3.31970.30664690.26618461X-RAY DIFFRACTION100
3.3197-3.38350.28634750.25148473X-RAY DIFFRACTION100
3.3835-3.45250.29014730.24218455X-RAY DIFFRACTION100
3.4525-3.52760.25974300.22988509X-RAY DIFFRACTION100
3.5276-3.60960.25714810.22078475X-RAY DIFFRACTION100
3.6096-3.69990.26444510.22348448X-RAY DIFFRACTION100
3.6999-3.79990.26724410.21318504X-RAY DIFFRACTION100
3.7999-3.91160.23224270.20668516X-RAY DIFFRACTION100
3.9116-4.03780.24134550.20078461X-RAY DIFFRACTION100
4.0378-4.18210.24574420.19998537X-RAY DIFFRACTION100
4.1821-4.34940.2494630.18768498X-RAY DIFFRACTION100
4.3494-4.54720.24254450.18458469X-RAY DIFFRACTION100
4.5472-4.78680.21174370.17618557X-RAY DIFFRACTION100
4.7868-5.08640.22464520.18068530X-RAY DIFFRACTION100
5.0864-5.47870.21984560.1838504X-RAY DIFFRACTION100
5.4787-6.02910.21184370.18588560X-RAY DIFFRACTION100
6.0291-6.89950.2254470.188556X-RAY DIFFRACTION100
6.8995-8.68480.1794610.15268588X-RAY DIFFRACTION100
8.6848-49.15480.23074520.2148636X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: -28.0049 Å / Origin y: -0.025 Å / Origin z: 145.821 Å
111213212223313233
T0.5165 Å20.0309 Å20.1384 Å2-0.4121 Å20.0842 Å2--0.4781 Å2
L0.2538 °20.0102 °20.2525 °2-0.0518 °20.0154 °2--0.274 °2
S-0.0025 Å °-0.0349 Å °-0.0518 Å °0.0291 Å °0.0217 Å °0.0063 Å °-0.0381 Å °0.035 Å °-0.0157 Å °
Refinement TLS groupSelection details: all

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