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- PDB-4pj0: Structure of T.elongatus Photosystem II, rows of dimers crystal p... -

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Basic information

Entry
Database: PDB / ID: 4pj0
TitleStructure of T.elongatus Photosystem II, rows of dimers crystal packing
Components
  • (Cytochrome b559 subunit ...) x 2
  • (Photosystem II ...) x 15
  • CP47 protein
  • Cytochrome c-550
  • Photosystem Q(B) protein 1
KeywordsOXIDOREDUCTASE / ELECTRON TRANSPORT / Membrane Protein / Photosystem II / C12E8
Function / homology
Function and homology information


thylakoid membrane / photosystem II / photosystem II reaction center / oxygen evolving activity / photosystem II assembly / photosystem II stabilization / cytochrome c-heme linkage / photosystem II oxygen evolving complex / oxidoreductase activity, acting on diphenols and related substances as donors, oxygen as acceptor / photosynthetic electron transport chain ...thylakoid membrane / photosystem II / photosystem II reaction center / oxygen evolving activity / photosystem II assembly / photosystem II stabilization / cytochrome c-heme linkage / photosystem II oxygen evolving complex / oxidoreductase activity, acting on diphenols and related substances as donors, oxygen as acceptor / photosynthetic electron transport chain / photosystem II / response to herbicide / chlorophyll binding / photosynthetic electron transport in photosystem II / electron transporter, transferring electrons within the cyclic electron transport pathway of photosynthesis activity / plasma membrane-derived thylakoid membrane / photosynthesis, light reaction / phosphate ion binding / extrinsic component of membrane / photosynthesis / respiratory electron transport chain / : / manganese ion binding / protein stabilization / electron transfer activity / iron ion binding / heme binding / integral component of membrane / metal ion binding
Similarity search - Function
photosynthetic oxygen evolving center domain / photosynthetic oxygen evolving center fold / Photosystem II, cytochrome c-550 precursor / Photosystem II 12 kDa extrinsic protein / Photosystem II reaction center protein H / Photosystem II PsbZ, reaction centre / photosystem ii from thermosynechococcus elongatus / Photosystem II CP47 reaction center protein / Photosystem II CP47 reaction center protein / Photosystem II cytochrome b559, alpha subunit ...photosynthetic oxygen evolving center domain / photosynthetic oxygen evolving center fold / Photosystem II, cytochrome c-550 precursor / Photosystem II 12 kDa extrinsic protein / Photosystem II reaction center protein H / Photosystem II PsbZ, reaction centre / photosystem ii from thermosynechococcus elongatus / Photosystem II CP47 reaction center protein / Photosystem II CP47 reaction center protein / Photosystem II cytochrome b559, alpha subunit / Photosystem II PsbY / Photosystem II protein Y (PsbY) / Photosystem II PsbU, oxygen evolving complex / Photosystem II 12 kDa extrinsic protein (PsbU) / Photosystem II reaction centre protein Ycf12 / Photosystem II complex subunit Ycf12 / Photosystem II PsbJ superfamily / PsbJ / Photosystem II PsbJ / Photosystem II PsbV, cytochrome c-550 precursor / Cytochrome c-550 domain / Cytochrome c-550 domain / Photosystem II cytochrome c-550 precursor / Photosystem II PsbX, type 1 subfamily / Photosystem II PsbZ, reaction centre / YCF9 / Photosystem II PsbZ superfamily / Photosystem II PsbM superfamily / Photosystem II reaction centre M protein (PsbM) / Manganese-stabilising protein / photosystem II polypeptide / Photosystem II PsbO, manganese-stabilising / Photosystem II PsbM / Photosystem II CP43 reaction centre protein superfamily / Photosystem II reaction centre T protein / PsbL protein / Photosystem II PsbL superfamily / Photosystem II PsbL / Photosystem II PsbT superfamily / Photosystem II PsbT / Photosystem II PsbK / Photosystem II CP43 reaction centre protein / Photosystem II 4 kDa reaction centre component / Photosystem II PsbK superfamily / Photosystem II PsbI / Photosystem II PsbI superfamily / Photosystem II reaction centre I protein (PSII 4.8 kDa protein) / Lumenal portion of Cytochrome b559, alpha (gene psbE) subunit / Photosystem II cytochrome b559, alpha subunit / Photosystem II D2 protein / Photosystem II cytochrome b559, alpha subunit superfamily / Cytochrome b559 subunits heme-binding site signature. / Photosystem II cytochrome b559, conserved site / Photosystem II CP47 reaction centre protein / Photosystem II cytochrome b559, alpha subunit, lumenal region / Photosystem II cytochrome b559, N-terminal / Cytochrome b559, alpha (gene psbE) and beta (gene psbF)subunits / Photosystem II cytochrome b559, beta subunit / Photosystem II protein D1 / Photosystem II PsbX / Photosystem II reaction centre X protein (PsbX) / Photosystem II 10 kDa phosphoprotein / Photosystem II reaction centre protein H / Photosystem II reaction centre protein H superfamily / Photosystem antenna protein-like superfamily / Photosystem antenna protein-like / Photosystem II protein / Outer membrane protein/outer membrane enzyme PagP, beta-barrel / Photosystem II protein D1/D2 superfamily / Photosynthetic reaction center proteins signature. / Photosynthetic reaction centre, L/M / Photosynthetic reaction centre protein / Porin / 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
Photosystem II reaction center protein Ycf12 / Photosystem II reaction center protein Z / Photosystem II CP47 reaction center protein / Photosystem II 12 kDa extrinsic protein / Photosystem II reaction center protein K / Photosystem II protein Y / Photosystem II reaction center protein I / Photosystem II CP43 reaction center protein / Photosystem II reaction center protein H / Photosystem II CP47 reaction center protein ...Photosystem II reaction center protein Ycf12 / Photosystem II reaction center protein Z / Photosystem II CP47 reaction center protein / Photosystem II 12 kDa extrinsic protein / Photosystem II reaction center protein K / Photosystem II protein Y / Photosystem II reaction center protein I / Photosystem II CP43 reaction center protein / Photosystem II reaction center protein H / Photosystem II CP47 reaction center protein / Photosystem II reaction center protein T / Cytochrome b559 subunit alpha / Cytochrome b559 subunit beta / Photosystem II reaction center protein L / Photosystem II D2 protein / Photosystem II reaction center protein M / BETA-CAROTENE / Photosystem II reaction center protein J / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / CHLOROPHYLL A / DIGALACTOSYL DIACYL GLYCEROL (DGDG) / : / HEME C / PROTOPORPHYRIN IX CONTAINING FE / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / CA-MN4-O5 CLUSTER / Photosystem II protein D1 1 / PHEOPHYTIN A / Chem-PL9 / Chem-SQD / Unknown ligand / BICARBONATE ION / Cytochrome c-550 / Photosystem II manganese-stabilizing polypeptide / Photosystem II reaction center X protein
Similarity search - Component
Biological speciesThermosynechococcus elongatus (Cyanobacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.437 Å
AuthorsHellmich, J. / Bommer, M. / Burkhardt, A. / Ibrahim, M. / Kern, J. / Meents, A. / Mueh, F. / Dobbek, H. / Zouni, A.
CitationJournal: Structure / Year: 2014
Title: Native-like Photosystem II Superstructure at 2.44 angstrom Resolution through Detergent Extraction from the Protein Crystal.
Authors: Hellmich, J. / Bommer, M. / Burkhardt, A. / Ibrahim, M. / Kern, J. / Meents, A. / Muh, F. / Dobbek, H. / Zouni, A.
History
DepositionMay 10, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 22, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 19, 2014Group: Structure summary
Revision 1.2Dec 24, 2014Group: Database references
Revision 2.0Mar 10, 2021Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Other / Source and taxonomy / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / citation / entity / entity_src_nat / pdbx_database_status / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_conn_angle / pdbx_struct_oper_list / pdbx_validate_chiral / struct_asym / struct_conn / struct_conn_type / struct_site
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.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 / _citation.journal_id_CSD / _entity_src_nat.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible / _pdbx_nonpoly_scheme.entity_id / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.pdb_mon_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.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _pdbx_struct_oper_list.symmetry_operation / _struct_asym.entity_id / _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 / _struct_site.details / _struct_site.pdbx_auth_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Photosystem Q(B) protein 1
B: CP47 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 X protein
Z: Photosystem II reaction center protein Z
a: Photosystem Q(B) protein 1
b: CP47 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
x: Photosystem II reaction center X protein
R: Photosystem II protein Y
r: Photosystem II protein Y
y: Photosystem II reaction center protein Ycf12
z: Photosystem II reaction center protein Z
hetero molecules


Theoretical massNumber of molelcules
Total (without water)747,423231
Polymers631,48540
Non-polymers115,938191
Water5,477304
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area276330 Å2
ΔGint-1842 kcal/mol
Surface area177440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)116.447, 218.889, 302.202
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 3 types, 6 molecules AaBbVv

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


Mass: 38265.625 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Thermosynechococcus elongatus (Cyanobacteria)
Strain: BP-1 / References: UniProt: P0A444, photosystem II
#2: Protein CP47 protein


Mass: 56656.457 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Thermosynechococcus elongatus (Cyanobacteria)
References: UniProt: Q9F1M3, UniProt: Q8DIQ1*PLUS, photosystem II
#16: Protein Cytochrome c-550 / Cytochrome c-549 / Cytochrome c550 / Low-potential cytochrome c


Mass: 18046.943 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Thermosynechococcus elongatus (Cyanobacteria)
Strain: BP-1 / References: UniProt: P0A386, photosystem II

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Photosystem II ... , 15 types, 30 molecules CcDdHhIiJjKkLlMmOoTtUuYyXxZzRr

#3: Protein Photosystem II CP43 protein /


Mass: 50287.500 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Thermosynechococcus elongatus (Cyanobacteria)
Strain: BP-1 / References: UniProt: Q8DIF8, photosystem II
#4: Protein Photosystem II D2 protein / / PSII D2 protein / Photosystem Q(A) protein


Mass: 39388.156 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Thermosynechococcus elongatus (Cyanobacteria)
Strain: BP-1 / References: UniProt: Q8CM25, photosystem II
#7: Protein Photosystem II reaction center protein H / / PSII-H


Mass: 7358.754 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Thermosynechococcus elongatus (Cyanobacteria)
Strain: BP-1 / References: UniProt: Q8DJ43, photosystem II
#8: Protein/peptide Photosystem II reaction center protein I / / PSII-I / PSII 4.4 kDa protein


Mass: 4410.245 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Thermosynechococcus elongatus (Cyanobacteria)
Strain: BP-1 / References: UniProt: Q8DJZ6, photosystem II
#9: Protein/peptide Photosystem II reaction center protein J / / PSII-J


Mass: 4105.908 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Thermosynechococcus elongatus (Cyanobacteria)
Strain: BP-1 / References: UniProt: P59087, photosystem II
#10: Protein/peptide Photosystem II reaction center protein K / / PSII-K


Mass: 5028.083 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Thermosynechococcus elongatus (Cyanobacteria)
Strain: BP-1 / References: UniProt: Q9F1K9, photosystem II
#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
Source: (natural) Thermosynechococcus elongatus (Cyanobacteria)
Strain: BP-1 / References: UniProt: Q8DIN8, photosystem II
#12: Protein/peptide Photosystem II reaction center protein M / / PSII-M


Mass: 3981.673 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Thermosynechococcus elongatus (Cyanobacteria)
Strain: BP-1 / References: UniProt: Q8DHA7, photosystem II
#13: Protein Photosystem II manganese-stabilizing polypeptide / / MSP


Mass: 29637.443 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Thermosynechococcus elongatus (Cyanobacteria)
Strain: BP-1 / References: UniProt: P0A431, photosystem II
#14: Protein/peptide Photosystem II reaction center protein T / / PSII-Tc


Mass: 3878.728 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Thermosynechococcus elongatus (Cyanobacteria)
Strain: BP-1 / References: UniProt: Q8DIQ0, photosystem II
#15: Protein Photosystem II 12 kDa extrinsic protein / / PS II complex 12 kDa extrinsic protein / PSII-U


Mass: 15030.986 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Thermosynechococcus elongatus (Cyanobacteria)
Strain: BP-1 / References: UniProt: Q9F1L5, photosystem II
#17: Protein/peptide Photosystem II reaction center protein Ycf12 /


Mass: 5039.143 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Thermosynechococcus elongatus (Cyanobacteria)
Strain: BP-1 / References: UniProt: Q8DJI1, photosystem II
#18: Protein/peptide Photosystem II reaction center X protein /


Mass: 4322.226 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Thermosynechococcus elongatus (Cyanobacteria)
Strain: BP-1 / References: UniProt: Q9F1R6, photosystem II
#19: Protein Photosystem II reaction center protein Z / / PSII-Z


Mass: 6766.187 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Thermosynechococcus elongatus (Cyanobacteria)
Strain: BP-1 / References: UniProt: Q8DHJ2, photosystem II
#20: Protein/peptide Photosystem II protein Y /


Mass: 4590.648 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Thermosynechococcus elongatus (Cyanobacteria)
Strain: BP-1 / References: UniProt: Q8DKM3, photosystem II

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

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


Mass: 9580.840 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Thermosynechococcus elongatus (Cyanobacteria)
Strain: BP-1 / References: UniProt: Q8DIP0, photosystem II
#6: Protein/peptide Cytochrome b559 subunit beta / / PSII reaction center subunit VI


Mass: 5067.900 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Thermosynechococcus elongatus (Cyanobacteria)
Strain: BP-1 / References: UniProt: Q8DIN9, photosystem II

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Sugars , 1 types, 8 molecules

#33: 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 , 16 types, 487 molecules

#21: Chemical ChemComp-OEX / CA-MN4-O5 CLUSTER


Mass: 339.827 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CaMn4O5
#22: Chemical ChemComp-FE / FE (III) ION / Iron


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe
#23: Chemical
ChemComp-LMG / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE


Mass: 787.158 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C45H86O10
#24: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


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


Mass: 893.489 Da / Num. of mol.: 70 / Source method: obtained synthetically / Formula: C55H72MgN4O5
#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.: 6 / Source method: obtained synthetically / Formula: C41H78O12S
#29: 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
#30: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: SO4
#31: Chemical ChemComp-BCT / BICARBONATE ION / Bicarbonate


Mass: 61.017 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CHO3 / Comment: pH buffer*YM
#32: Chemical...
ChemComp-UNL / UNKNOWN LIGAND


Num. of mol.: 29 / Source method: obtained synthetically
#34: Chemical
ChemComp-PHO / PHEOPHYTIN A / Pheophytin


Mass: 871.200 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C55H74N4O5
#35: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#36: Chemical ChemComp-HEC / HEME C / Heme C


Mass: 618.503 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H34FeN4O4
#37: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 304 / Source method: isolated from a natural source / Formula: H2O

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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: 3.04 Å3/Da / Density % sol: 59.47 %
Crystal growTemperature: 293 K / Method: evaporation / pH: 7.5
Details: Batch crystallisation: 2 mM Chl a equivalent of PSIIcc mixed 1:1 with: 0.1 M TRIS (pH 7.5), 0.1 M (NH4)2SO4, 15 - 18 % PEG 5000 MME, post-crystallisation dehydration

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Type: OTHER / Wavelength: 1.196 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Mar 22, 2013
RadiationMonochromator: Si-111 double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.196 Å / Relative weight: 1
ReflectionResolution: 2.44→49.12 Å / Num. obs: 282213 / % possible obs: 98.4 % / Observed criterion σ(I): 2 / Redundancy: 6 % / Biso Wilson estimate: 39.1 Å2 / Rmerge(I) obs: 0.094 / Net I/σ(I): 14.7
Reflection shellResolution: 2.44→2.524 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.6979 / Mean I/σ(I) obs: 1.93 / % possible all: 89.5

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.9_1690) / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3ARC

3arc
PDB Unreleased entry


Resolution: 2.437→49.123 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 26.67 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2556 14110 5 %Random selection
Rwork0.2159 ---
obs0.2179 282177 98.36 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.437→49.123 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms41409 0 8522 304 50235
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00751856
X-RAY DIFFRACTIONf_angle_d0.96571128
X-RAY DIFFRACTIONf_dihedral_angle_d13.23621036
X-RAY DIFFRACTIONf_chiral_restr0.0367144
X-RAY DIFFRACTIONf_plane_restr0.00410897
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.437-2.46490.38323860.32147331X-RAY DIFFRACTION82
2.4649-2.49390.36784400.31078368X-RAY DIFFRACTION93
2.4939-2.52430.34594460.29658487X-RAY DIFFRACTION94
2.5243-2.55620.36074530.27528602X-RAY DIFFRACTION95
2.5562-2.58990.3194560.27318652X-RAY DIFFRACTION96
2.5899-2.62540.32474590.26418713X-RAY DIFFRACTION97
2.6254-2.66290.28864660.25358861X-RAY DIFFRACTION98
2.6629-2.70260.30934680.26088900X-RAY DIFFRACTION99
2.7026-2.74480.34984690.25918908X-RAY DIFFRACTION99
2.7448-2.78980.31094710.24398951X-RAY DIFFRACTION99
2.7898-2.83790.29354740.23399001X-RAY DIFFRACTION99
2.8379-2.88950.30064730.2448983X-RAY DIFFRACTION100
2.8895-2.94510.29534750.24279015X-RAY DIFFRACTION100
2.9451-3.00520.29654770.23599059X-RAY DIFFRACTION100
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