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- PDB-4il6: Structure of Sr-substituted photosystem II -

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Basic information

Entry
Database: PDB / ID: 4il6
TitleStructure of Sr-substituted photosystem II
Components
  • (Cytochrome b559 subunit ...) x 2
  • (Photosystem II ...) x 16
  • Cytochrome c-550
  • Photosystem Q(B) protein
KeywordsELECTRON TRANSPORT / Photosystem II / Electron transfer / Light-Driven Water Oxidation / Membrane-Protein Complex / Oxygen Evolution / Oxygen-Evolving Complex / Proton-Coupled Electron Transfer / Photosynthesis / Reaction Centre / Sr-Substituted Photosystem II / Substrate Water molecule / Trans-Membrane Alpha Helix
Function / homology
Function and homology information


photosystem II assembly / photosystem II stabilization / oxygen evolving activity / photosystem II oxygen evolving complex / photosystem II / photosystem II reaction center / oxidoreductase activity, acting on diphenols and related substances as donors, oxygen as acceptor / photosynthetic electron transport chain / response to herbicide / photosystem II ...photosystem II assembly / photosystem II stabilization / oxygen evolving activity / photosystem II oxygen evolving complex / photosystem II / photosystem II reaction center / oxidoreductase activity, acting on diphenols and related substances as donors, oxygen as acceptor / photosynthetic electron transport chain / response to herbicide / photosystem II / photosynthetic electron transport in photosystem II / extrinsic component of membrane / chlorophyll binding / plasma membrane-derived thylakoid membrane / photosynthesis, light reaction / electron transporter, transferring electrons within the cyclic electron transport pathway of photosynthesis activity / phosphate ion binding / photosynthesis / respiratory electron transport chain / manganese ion binding / electron transfer activity / protein stabilization / iron ion binding / heme binding / metal ion binding
Similarity search - Function
photosynthetic oxygen evolving center fold / photosynthetic oxygen evolving center domain / Photosystem II, cytochrome c-550 precursor / Photosystem II 12 kDa extrinsic protein / Photosystem II PsbZ, reaction centre / Photosystem II reaction center protein H / photosystem ii from thermosynechococcus elongatus / Photosystem II cytochrome b559, alpha subunit / Photosystem II CP47 reaction center protein / Photosystem II CP47 reaction center protein ...photosynthetic oxygen evolving center fold / photosynthetic oxygen evolving center domain / Photosystem II, cytochrome c-550 precursor / Photosystem II 12 kDa extrinsic protein / Photosystem II PsbZ, reaction centre / Photosystem II reaction center protein H / photosystem ii from thermosynechococcus elongatus / Photosystem II cytochrome b559, alpha subunit / Photosystem II CP47 reaction center protein / Photosystem II CP47 reaction center protein / Single helix bin / Photosystem II protein Y (PsbY) / Photosystem II PsbY / Photosystem II PsbU, oxygen evolving complex / Photosystem II 12 kDa extrinsic protein (PsbU) / Photosystem II PsbV, cytochrome c-550 precursor / Photosystem II cytochrome c-550 precursor / Cytochrome c-550 domain / Cytochrome c-550 domain / Photosystem II PsbJ / Photosystem II PsbJ superfamily / PsbJ / Photosystem II reaction centre protein Ycf12 / Photosystem II complex subunit Ycf12 / Photosystem II PsbX, type 1 subfamily / Photosystem II PsbO, manganese-stabilising / Manganese-stabilising protein / photosystem II polypeptide / Photosystem II reaction centre M protein (PsbM) / Photosystem II PsbM superfamily / Photosystem II PsbZ, reaction centre / Photosystem II PsbZ superfamily / YCF9 / Photosystem II PsbM / Photosystem II PsbX / Photosystem II reaction centre X protein (PsbX) / Photosystem II PsbT / Photosystem II PsbL / Photosystem II PsbL superfamily / Photosystem II PsbT superfamily / Photosystem II CP43 reaction centre protein superfamily / Photosystem II reaction centre T protein / PsbL protein / Photosystem II PsbK / Photosystem II CP43 reaction centre protein / Photosystem II PsbK superfamily / Photosystem II 4 kDa reaction centre component / Photosystem II CP47 reaction centre protein / Photosystem II PsbI / Photosystem II PsbI superfamily / Photosystem II reaction centre I protein (PSII 4.8 kDa protein) / Photosystem II reaction centre protein H / Photosystem II protein D1 / Photosystem II D2 protein / Photosystem II cytochrome b559, conserved site / Photosystem II cytochrome b559, alpha subunit / Photosystem II cytochrome b559, beta subunit / Photosystem II cytochrome b559, N-terminal / Photosystem II cytochrome b559, alpha subunit, lumenal region / Photosystem II reaction centre protein H superfamily / Photosystem II cytochrome b559, alpha subunit superfamily / Cytochrome b559, alpha (gene psbE) and beta (gene psbF)subunits / Lumenal portion of Cytochrome b559, alpha (gene psbE) subunit / Photosystem II 10 kDa phosphoprotein / Cytochrome b559 subunits heme-binding site signature. / Photosystem antenna protein-like / Photosystem antenna protein-like superfamily / Photosystem II protein / Outer membrane protein/outer membrane enzyme PagP, beta-barrel / Porin / Photosynthetic reaction centre, L/M / Photosystem II protein D1/D2 superfamily / Photosynthetic reaction centre protein / Photosynthetic reaction center proteins signature. / Cytochrome c-like domain / Cytochrome Bc1 Complex; Chain D, domain 2 / Cytochrome c family profile. / Cytochrome c-like domain / Cytochrome c-like domain superfamily / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / DNA polymerase; domain 1 / Helix Hairpins / Arc Repressor Mutant, subunit A / Roll / Up-down Bundle / Beta Barrel / 2-Layer Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
BETA-CAROTENE / BICARBONATE ION / CHLOROPHYLL A / DIGALACTOSYL DIACYL GLYCEROL (DGDG) / : / PROTOPORPHYRIN IX CONTAINING FE / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / SR-MN4-O5 CLUSTER / PHEOPHYTIN A ...BETA-CAROTENE / BICARBONATE ION / CHLOROPHYLL A / DIGALACTOSYL DIACYL GLYCEROL (DGDG) / : / PROTOPORPHYRIN IX CONTAINING FE / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / SR-MN4-O5 CLUSTER / PHEOPHYTIN A / Chem-PL9 / Chem-SQD / Unknown ligand / Photosystem II CP47 reaction center protein / Photosystem II extrinsic protein O / Photosystem II reaction center protein Psb30 / Photosystem II reaction center protein X / Photosystem II reaction center protein Z / Photosystem II CP43 reaction center protein / Photosystem II D2 protein / Photosystem II extrinsic protein V / Cytochrome b559 subunit alpha / Cytochrome b559 subunit beta / Photosystem II reaction center protein I / Photosystem II reaction center protein L / Photosystem II reaction center protein M / Photosystem II reaction center protein T / Photosystem II reaction center protein H / Photosystem II reaction center protein K / Photosystem II protein D1 / Photosystem II extrinsic protein U / Photosystem II reaction center protein J / Photosystem II reaction center protein Y
Similarity search - Component
Biological speciesThermosynechococcus vulcanus (bacteria)
Thermosynechococcus elongatus BP-1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsKoua, F.H.M. / Umena, Y. / Kawakami, K. / Kamiya, N. / Shen, J.R.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2013
Title: Structure of Sr-substituted photosystem II at 2.1 A resolution and its implications in the mechanism of water oxidation
Authors: Koua, F.H. / Umena, Y. / Kawakami, K. / Shen, J.R.
History
DepositionDec 29, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 6, 2013Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2013Group: Database references
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software
Revision 1.3Jul 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.type ..._chem_comp.name / _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.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.0Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Non-polymer description / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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 Q(B) protein
B: Photosystem II core light harvesting protein
C: Photosystem II CP43 protein
D: Photosystem II D2 protein
E: Cytochrome b559 subunit alpha
F: Cytochrome b559 subunit beta
H: Photosystem II reaction center protein H
I: Photosystem II reaction center protein I
J: Photosystem II reaction center protein J
K: Photosystem II reaction center protein K
L: Photosystem II reaction center protein L
M: Photosystem II reaction center protein M
O: Photosystem II manganese-stabilizing polypeptide
T: Photosystem II reaction center protein T
U: Photosystem II 12 kDa extrinsic protein
V: Cytochrome c-550
Y: Photosystem II reaction center protein ycf12
X: Photosystem II reaction center protein X
Z: Photosystem II reaction center protein Z
R: Photosystem II protein Y
a: Photosystem Q(B) protein
b: Photosystem II core light harvesting protein
c: Photosystem II CP43 protein
d: Photosystem II D2 protein
e: Cytochrome b559 subunit alpha
f: Cytochrome b559 subunit beta
h: Photosystem II reaction center protein H
i: Photosystem II reaction center protein I
j: Photosystem II reaction center protein J
k: Photosystem II reaction center protein K
l: Photosystem II reaction center protein L
m: Photosystem II reaction center protein M
o: Photosystem II manganese-stabilizing polypeptide
t: Photosystem II reaction center protein T
u: Photosystem II 12 kDa extrinsic protein
v: Cytochrome c-550
y: Photosystem II reaction center protein ycf12
x: Photosystem II reaction center protein X
z: Photosystem II reaction center protein Z
hetero molecules


Theoretical massNumber of molelcules
Total (without water)719,094298
Polymers587,40939
Non-polymers131,685259
Water36,6972037
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)121.860, 228.790, 285.760
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Detailsbiological unit is the same as asym.

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Components

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Protein , 2 types, 4 molecules AaVv

#1: Protein Photosystem Q(B) protein / 32 kDa thylakoid membrane protein / Photosystem II protein D1


Mass: 37029.234 Da / Num. of mol.: 2 / Fragment: UNP residues 11-344 / Source method: isolated from a natural source / Details: Cell / Source: (natural) Thermosynechococcus vulcanus (bacteria) / References: UniProt: P51765, photosystem II
#16: Protein Cytochrome c-550 / Cytochrome c550 / Low-potential cytochrome c


Mass: 15148.255 Da / Num. of mol.: 2 / Fragment: UNP residues 27-163 / Source method: isolated from a natural source / Details: Cell / Source: (natural) Thermosynechococcus vulcanus (bacteria) / References: UniProt: P0A387

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Photosystem II ... , 16 types, 31 molecules BbCcDdHhIiJjKkLlMmOoTtUuYyXxZzR

#2: Protein Photosystem II core light harvesting protein /


Mass: 56068.742 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: Cell / Source: (natural) Thermosynechococcus vulcanus (bacteria) / References: UniProt: D0VWR1*PLUS
#3: Protein Photosystem II CP43 protein /


Mass: 49207.250 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: Cell / Source: (natural) Thermosynechococcus vulcanus (bacteria) / References: UniProt: D0VWR7*PLUS
#4: Protein Photosystem II D2 protein / / PSII D2 protein / Photosystem Q(A) protein


Mass: 38404.949 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: Cell / Source: (natural) Thermosynechococcus vulcanus (bacteria) / References: UniProt: D0VWR8*PLUS, photosystem II
#7: Protein Photosystem II reaction center protein H / / PSII-H


Mass: 7057.349 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: Cell / Source: (natural) Thermosynechococcus vulcanus (bacteria) / References: UniProt: P19052*PLUS
#8: Protein/peptide Photosystem II reaction center protein I / / PSII-I / PSII 4.4 kDa protein


Mass: 4195.983 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: Cell / Source: (natural) Thermosynechococcus vulcanus (bacteria) / References: UniProt: P12240*PLUS
#9: Protein/peptide Photosystem II reaction center protein J / / PSII-J


Mass: 3756.439 Da / Num. of mol.: 2 / Fragment: UNP residues 4-40 / Source method: isolated from a natural source / Details: Cell / Source: (natural) Thermosynechococcus vulcanus (bacteria) / References: UniProt: Q7DGD4
#10: Protein/peptide Photosystem II reaction center protein K / / PSII-K


Mass: 4101.911 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: Cell / Source: (natural) Thermosynechococcus vulcanus (bacteria) / References: UniProt: P19054*PLUS
#11: Protein/peptide Photosystem II reaction center protein L / / PSII-L / PSII 5 kDa protein


Mass: 4299.044 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: Cell / Source: (natural) Thermosynechococcus vulcanus (bacteria) / References: UniProt: P12241
#12: Protein/peptide Photosystem II reaction center protein M / / PSII-M


Mass: 3835.527 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: Cell / Source: (natural) Thermosynechococcus vulcanus (bacteria) / References: UniProt: P12312*PLUS
#13: Protein Photosystem II manganese-stabilizing polypeptide /


Mass: 26651.707 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: Cell / Source: (natural) Thermosynechococcus vulcanus (bacteria) / References: UniProt: D0VWR2*PLUS
#14: Protein/peptide Photosystem II reaction center protein T / / PSII-T / PSII-Tc


Mass: 3777.559 Da / Num. of mol.: 2 / Fragment: UNP residues 2-31 / Source method: isolated from a natural source / Details: Cell / Source: (natural) Thermosynechococcus vulcanus (bacteria) / References: UniProt: P12313
#15: Protein Photosystem II 12 kDa extrinsic protein / / PS II complex 12 kDa extrinsic protein / PSII-U


Mass: 10966.317 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: Cell / Source: (natural) Thermosynechococcus vulcanus (bacteria) / References: UniProt: P56152*PLUS
#17: Protein/peptide Photosystem II reaction center protein ycf12 /


Mass: 3228.035 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: Cell / Source: (natural) Thermosynechococcus vulcanus (bacteria) / References: UniProt: D0VWR3*PLUS
#18: Protein/peptide Photosystem II reaction center protein X /


Mass: 4191.030 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: Cell / Source: (natural) Thermosynechococcus vulcanus (bacteria) / References: UniProt: D0VWR4*PLUS
#19: Protein Photosystem II reaction center protein Z / / PSII-Z


Mass: 6794.197 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: Cell / Source: (natural) Thermosynechococcus vulcanus (bacteria) / References: UniProt: D0VWR5*PLUS
#20: Protein/peptide Photosystem II protein Y /


Mass: 3859.732 Da / Num. of mol.: 1 / Fragment: UNP residues 2-35 / Source method: isolated from a natural source / Details: Cell
Source: (natural) Thermosynechococcus elongatus BP-1 (bacteria)
Strain: BP-1 / References: UniProt: Q8DKM3

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Cytochrome b559 subunit ... , 2 types, 4 molecules EeFf

#5: Protein Cytochrome b559 subunit alpha / / PSII reaction center subunit V


Mass: 9192.334 Da / Num. of mol.: 2 / Fragment: UNP residues 4-83 / Source method: isolated from a natural source / Details: Cell / Source: (natural) Thermosynechococcus vulcanus (bacteria) / References: UniProt: P12238
#6: Protein/peptide Cytochrome b559 subunit beta / / PSII reaction center subunit VI


Mass: 3868.611 Da / Num. of mol.: 2 / Fragment: UNP residues 12-45 / Source method: isolated from a natural source / Details: Cell / Source: (natural) Thermosynechococcus vulcanus (bacteria) / References: UniProt: P12239

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Sugars , 3 types, 40 molecules

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


Type: D-saccharide / Mass: 510.615 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: C24H46O11 / Comment: detergent*YM
#35: 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.: 17 / Source method: obtained synthetically / Formula: C13H26O5S / Comment: detergent*YM
#36: Sugar
ChemComp-DGD / DIGALACTOSYL DIACYL GLYCEROL (DGDG)


Type: saccharideCarbohydrate / Mass: 949.299 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C51H96O15

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Non-polymers , 17 types, 2256 molecules

#21: Chemical ChemComp-OER / SR-MN4-O5 CLUSTER / Mn4SrOt5-cluster


Mass: 387.369 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn4O5Sr
#22: Chemical ChemComp-FE2 / FE (II) ION


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


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#24: Chemical...
ChemComp-CLA / CHLOROPHYLL A / Chlorophyll a


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


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


Mass: 536.873 Da / Num. of mol.: 22 / Source method: obtained synthetically / Formula: C40H56
#27: Chemical
ChemComp-PL9 / 2,3-DIMETHYL-5-(3,7,11,15,19,23,27,31,35-NONAMETHYL-2,6,10,14,18,22,26,30,34-HEXATRIACONTANONAENYL-2,5-CYCLOHEXADIENE-1,4-DIONE-2,3-DIMETHYL-5-SOLANESYL-1,4-BENZOQUINONE / PLASTOQUINONE 9 / Plastoquinone


Mass: 749.201 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C53H80O2
#28: Chemical
ChemComp-SQD / 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL / SULFOQUINOVOSYLDIACYLGLYCEROL


Mass: 795.116 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C41H78O12S
#29: Chemical
ChemComp-LMG / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE


Mass: 787.158 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C45H86O10
#30: Chemical...
ChemComp-DMS / DIMETHYL SULFOXIDE / Dimethyl sulfoxide


Mass: 78.133 Da / Num. of mol.: 35 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#31: Chemical...
ChemComp-UNL / UNKNOWN LIGAND


Num. of mol.: 24 / Source method: obtained synthetically
#33: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C3H8O3
#34: Chemical
ChemComp-LHG / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / Phosphatidylglycerol


Mass: 722.970 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C38H75O10P / Comment: phospholipid*YM
#37: Chemical ChemComp-BCT / BICARBONATE ION / Bicarbonate


Mass: 61.017 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CHO3 / Comment: pH buffer*YM
#38: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


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


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#40: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 2037 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsPRO279/CHAIN A(a) and LEU8/CHAIN M(m) HAVE BEEN CONFIRMED FROM THE ELECTRON DENSITY MAP. SEQUENCES ...PRO279/CHAIN A(a) and LEU8/CHAIN M(m) HAVE BEEN CONFIRMED FROM THE ELECTRON DENSITY MAP. SEQUENCES FOR THE CHAINS B(b), C(c), D(d), REMARK 999 H(h), I(i), K(k), M(m), O(o), U(u), Y(y), X(x), Z(z) ARE BASED ON BOTH ELECTRON DENSITY MAP AND THE SEQUENCES FROM THE CLOSELY RELATED SOURCE THERMOSYNECHOCOCCUS ELONGATUS.

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 3.39 Å3/Da / Density % sol: 63.72 %
Crystal growTemperature: 285 K / Method: oil-microbatch method / pH: 6.1
Details: Sr-PSII protein was crystallised in 4.5-5.5%PEG1450, 20mM Mes-NaOH, pH 6.1, 20mM NaCl, 3-4mM SrCl2, Oil-Microbatch Method, temperature 285K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.76 Å
DetectorType: MAR225HE / Detector: CCD / Date: Jun 17, 2011
RadiationMonochromator: double-crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.76 Å / Relative weight: 1
ReflectionResolution: 2.1→20 Å / Num. all: 460677 / Num. obs: 437644 / % possible obs: 99.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1 / Redundancy: 7.4 % / Biso Wilson estimate: 40.8 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 18.1
Reflection shellResolution: 2.1→2.15 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.8 / Mean I/σ(I) obs: 2.6 / Num. unique all: 460678 / % possible all: 100

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
REFMAC5.6.0117refinement
PDB_EXTRACT3.11data extraction
HKL-2000data collection
XDSdata reduction
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3ARC

3arc
PDB Unreleased entry


Resolution: 2.1→19.96 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.95 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 4.367 / SU ML: 0.114 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.184 / ESU R Free: 0.154 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2053 23034 5 %RANDOM
Rwork0.1761 ---
all0.198 460678 --
obs0.1776 437644 99.77 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 116.41 Å2 / Biso mean: 37.6797 Å2 / Biso min: 16.83 Å2
Baniso -1Baniso -2Baniso -3
1-2.79 Å20 Å20 Å2
2---1.08 Å20 Å2
3----1.71 Å2
Refinement stepCycle: LAST / Resolution: 2.1→19.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms41495 0 9666 2037 53198
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.02553385
X-RAY DIFFRACTIONr_angle_refined_deg2.972.69672919
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.05655348
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.29823.2131877
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.504156581
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.05315230
X-RAY DIFFRACTIONr_chiral_restr0.0740.27494
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02137848
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.288 1623 -
Rwork0.266 30728 -
all-32351 -
obs-460677 99.84 %

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