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- EMDB-31400: STRUCTURE OF PHOTOSYNTHETIC LH1-RC SUPER-COMPLEX OF RHODOBACTER S... -

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Basic information

Entry
Database: EMDB / ID: EMD-31400
TitleSTRUCTURE OF PHOTOSYNTHETIC LH1-RC SUPER-COMPLEX OF RHODOBACTER SPHAEROIDES MONOMER
Map data
Sample
  • Complex: Photosynthetic LH1-RC complex from the purple phototrophic bacterium Rhodobacter sphaeroides monomer
    • Protein or peptide: x 8 types
  • Ligand: x 9 types
Function / homology
Function and homology information


organelle inner membrane / plasma membrane light-harvesting complex / bacteriochlorophyll binding / photosynthesis, light reaction / electron transporter, transferring electrons within the cyclic electron transport pathway of photosynthesis activity / membrane => GO:0016020 / metal ion binding / plasma membrane
Similarity search - Function
Intrinsic membrane protein family, PufX / Intrinsic membrane protein PufX / Antenna complex, beta subunit, conserved site / Antenna complexes beta subunits signature. / Antenna complex, alpha subunit / Antenna complex, beta domain superfamily / Antenna complex, alpha subunit conserved site / Antenna complexes alpha subunits signature. / Light-harvesting protein B beta chain / Antenna complex, alpha/beta subunit ...Intrinsic membrane protein family, PufX / Intrinsic membrane protein PufX / Antenna complex, beta subunit, conserved site / Antenna complexes beta subunits signature. / Antenna complex, alpha subunit / Antenna complex, beta domain superfamily / Antenna complex, alpha subunit conserved site / Antenna complexes alpha subunits signature. / Light-harvesting protein B beta chain / Antenna complex, alpha/beta subunit / Light-harvesting complex / Antenna complex alpha/beta subunit
Similarity search - Domain/homology
Uncharacterized protein / Uncharacterized protein / Light-harvesting protein B-875 alpha chain / Antenna pigment protein beta chain
Similarity search - Component
Biological speciesRhodobacter sphaeroides f. sp. denitrificans (bacteria) / Rhodobacter sphaeroides (bacteria) / Rhodopseudomonas sphaeroides (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.94 Å
AuthorsTani K / Nagashima VP / Kanno R / Kawamura S / Kikuchi R / Ji X-C / Hall M / Yu L-J / Kimura Y / Madigan MT ...Tani K / Nagashima VP / Kanno R / Kawamura S / Kikuchi R / Ji X-C / Hall M / Yu L-J / Kimura Y / Madigan MT / Mizoguchi A / Humbel BM / Wang-Otomo Z-Y
Funding support Japan, 6 items
OrganizationGrant numberCountry
Japan Agency for Medical Research and Development (AMED)JP21am0101118 Japan
Japan Agency for Medical Research and Development (AMED)JP21am0101116 Japan
Japan Society for the Promotion of Science (JSPS)JP16H04174 Japan
Japan Society for the Promotion of Science (JSPS)JP18H05153 Japan
Japan Society for the Promotion of Science (JSPS)20H05086 Japan
Japan Society for the Promotion of Science (JSPS)20H02856 Japan
CitationJournal: Nat Commun / Year: 2021
Title: A previously unrecognized membrane protein in the Rhodobacter sphaeroides LH1-RC photocomplex.
Authors: Kazutoshi Tani / Kenji V P Nagashima / Ryo Kanno / Saki Kawamura / Riku Kikuchi / Malgorzata Hall / Long-Jiang Yu / Yukihiro Kimura / Michael T Madigan / Akira Mizoguchi / Bruno M Humbel / ...Authors: Kazutoshi Tani / Kenji V P Nagashima / Ryo Kanno / Saki Kawamura / Riku Kikuchi / Malgorzata Hall / Long-Jiang Yu / Yukihiro Kimura / Michael T Madigan / Akira Mizoguchi / Bruno M Humbel / Zheng-Yu Wang-Otomo /
Abstract: Rhodobacter (Rba.) sphaeroides is the most widely used model organism in bacterial photosynthesis. The light-harvesting-reaction center (LH1-RC) core complex of this purple phototroph is ...Rhodobacter (Rba.) sphaeroides is the most widely used model organism in bacterial photosynthesis. The light-harvesting-reaction center (LH1-RC) core complex of this purple phototroph is characterized by the co-existence of monomeric and dimeric forms, the presence of the protein PufX, and approximately two carotenoids per LH1 αβ-polypeptides. Despite many efforts, structures of the Rba. sphaeroides LH1-RC have not been obtained at high resolutions. Here we report a cryo-EM structure of the monomeric LH1-RC from Rba. sphaeroides strain IL106 at 2.9 Å resolution. The LH1 complex forms a C-shaped structure composed of 14 αβ-polypeptides around the RC with a large ring opening. From the cryo-EM density map, a previously unrecognized integral membrane protein, referred to as protein-U, was identified. Protein-U has a U-shaped conformation near the LH1-ring opening and was annotated as a hypothetical protein in the Rba. sphaeroides genome. Deletion of protein-U resulted in a mutant strain that expressed a much-reduced amount of the dimeric LH1-RC, indicating an important role for protein-U in dimerization of the LH1-RC complex. PufX was located opposite protein-U on the LH1-ring opening, and both its position and conformation differed from that of previous reports of dimeric LH1-RC structures obtained at low-resolution. Twenty-six molecules of the carotenoid spheroidene arranged in two distinct configurations were resolved in the Rba. sphaeroides LH1 and were positioned within the complex to block its channels. Our findings offer an exciting new view of the core photocomplex of Rba. sphaeroides and the connections between structure and function in bacterial photocomplexes in general.
History
DepositionJun 5, 2021-
Header (metadata) releaseNov 10, 2021-
Map releaseNov 10, 2021-
UpdateNov 17, 2021-
Current statusNov 17, 2021Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.064
  • Imaged by UCSF Chimera
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  • Surface view colored by height
  • Surface level: 0.064
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7f0l
  • Surface level: 0.064
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_31400.png

Downloads & links

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Map

FileDownload / File: emd_31400.map.gz / Format: CCP4 / Size: 83.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.094 Å
Density
Contour LevelBy AUTHOR: 0.064 / Movie #1: 0.064
Minimum - Maximum-0.28797254 - 0.46609327
Average (Standard dev.)2.391604e-05 (±0.01598618)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions280280280
Spacing280280280
CellA=B=C: 306.32 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0941.0941.094
M x/y/z280280280
origin x/y/z0.0000.0000.000
length x/y/z306.320306.320306.320
α/β/γ90.00090.00090.000
start NX/NY/NZ-300-300-300
NX/NY/NZ600600600
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS280280280
D min/max/mean-0.2880.4660.000

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Supplemental data

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Sample components

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Entire : Photosynthetic LH1-RC complex from the purple phototrophic bacter...

EntireName: Photosynthetic LH1-RC complex from the purple phototrophic bacterium Rhodobacter sphaeroides monomer
Components
  • Complex: Photosynthetic LH1-RC complex from the purple phototrophic bacterium Rhodobacter sphaeroides monomer
    • Protein or peptide: Photosynthetic reaction center L subunit
    • Protein or peptide: Reaction center protein M chainPhotosynthetic reaction centre
    • Protein or peptide: Reaction center protein H chainPhotosynthetic reaction centre
    • Protein or peptide: Light-harvesting protein B-875 alpha chain
    • Protein or peptide: Antenna pigment protein beta chainPhotosynthetic pigment
    • Protein or peptide: Light-harvesting protein B-875 alpha chain
    • Protein or peptide: PufX
    • Protein or peptide: protein-U
  • Ligand: BACTERIOCHLOROPHYLL ABacteriochlorophyll
  • Ligand: BACTERIOPHEOPHYTIN A
  • Ligand: UBIQUINONE-10Coenzyme Q10
  • Ligand: (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE
  • Ligand: LAURYL DIMETHYLAMINE-N-OXIDE
  • Ligand: FE (III) ION
  • Ligand: SPHEROIDENE
  • Ligand: DODECYL-BETA-D-MALTOSIDE
  • Ligand: CARDIOLIPIN

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Supramolecule #1: Photosynthetic LH1-RC complex from the purple phototrophic bacter...

SupramoleculeName: Photosynthetic LH1-RC complex from the purple phototrophic bacterium Rhodobacter sphaeroides monomer
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#8
Source (natural)Organism: Rhodobacter sphaeroides f. sp. denitrificans (bacteria)
Strain: IL106

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Macromolecule #1: Photosynthetic reaction center L subunit

MacromoleculeName: Photosynthetic reaction center L subunit / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Rhodobacter sphaeroides (bacteria)
Molecular weightTheoretical: 31.491611 KDa
SequenceString: MALLSFERKY RVPGGTLVGG NLFDFWVGPF YVGFFGVATF FFAALGIILI AWSAVLQGTW NPQLISVYPP ALEYGLGGAP LAKGGLWQI ITICATGAFV SWALREVEIC RKLGIGYHIP FAFAFAILAY LTLVLFRPVM MGAWGYAFPY GIWTHLDWVS N TGYTYGNF ...String:
MALLSFERKY RVPGGTLVGG NLFDFWVGPF YVGFFGVATF FFAALGIILI AWSAVLQGTW NPQLISVYPP ALEYGLGGAP LAKGGLWQI ITICATGAFV SWALREVEIC RKLGIGYHIP FAFAFAILAY LTLVLFRPVM MGAWGYAFPY GIWTHLDWVS N TGYTYGNF HYNPAHMIAI TFFFTNALAL ALHGALVLSA ANPEKGKEMR TPDHEDTFFR DLVGYSIGTL GIHRLGLLLS LS AVFFSAL CMIITGTIWF DQWVDWWQWW VKLPWWANIP GGING

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Macromolecule #2: Reaction center protein M chain

MacromoleculeName: Reaction center protein M chain / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Rhodobacter sphaeroides (bacteria)
Molecular weightTheoretical: 34.543762 KDa
SequenceString: MAEYQNIFTQ VQVRGPADLG MTEDVNLANR SGVGPFSTLL GWFGNAQLGP IYLGSLGVLS LFSGLMWFFT IGIWFWYQAG WNPAVFLRD LFFFSLEPPA PEYGLSFAAP LKEGGLWLIA SFFMFVAVWS WWGRTYLRAQ ALGMGKHTAW AFLSAIWLWM V LGFIRPIL ...String:
MAEYQNIFTQ VQVRGPADLG MTEDVNLANR SGVGPFSTLL GWFGNAQLGP IYLGSLGVLS LFSGLMWFFT IGIWFWYQAG WNPAVFLRD LFFFSLEPPA PEYGLSFAAP LKEGGLWLIA SFFMFVAVWS WWGRTYLRAQ ALGMGKHTAW AFLSAIWLWM V LGFIRPIL MGSWSEAVPY GIFSHLDWTN NFSLVHGNLF YNPFHGLSIA FLYGSALLFA MHGATILAVS RFGGERELEQ IA DRGTAAE RAALFWRWTM GFNATMEGIH RWAIWMAVLV TLTGGIGILL SGTVVDNWYV WGQNHGMAPL N

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Macromolecule #3: Reaction center protein H chain

MacromoleculeName: Reaction center protein H chain / type: protein_or_peptide / ID: 3 / Details: WP_069330428.1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Rhodopseudomonas sphaeroides (bacteria)
Molecular weightTheoretical: 28.09135 KDa
SequenceString: MVGVTAFGNF DLASLAIYSF WIFLAGLIYY LQTENMREGY PLENEDGTPA ANQGPFPLPK PKTFILPHGR GTLTVPGPES EDRPIALAR TAVSEGFPHA PTGDPMKDGV GPASWVARRD LPELDGHGHN KIKPMKAAAG FYVSAGKNPI GLPVRGCDLE I AGKVVDIW ...String:
MVGVTAFGNF DLASLAIYSF WIFLAGLIYY LQTENMREGY PLENEDGTPA ANQGPFPLPK PKTFILPHGR GTLTVPGPES EDRPIALAR TAVSEGFPHA PTGDPMKDGV GPASWVARRD LPELDGHGHN KIKPMKAAAG FYVSAGKNPI GLPVRGCDLE I AGKVVDIW VDIPEQMARF LEVELKDGST RLLPMQMVKV QSNRVHVNAL SSDLFAGIPT IKSPTEVTLL EEDKICGYVA GG LMYAAPK RKSVVAAMLA EYA

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Macromolecule #4: Light-harvesting protein B-875 alpha chain

MacromoleculeName: Light-harvesting protein B-875 alpha chain / type: protein_or_peptide / ID: 4 / Details: WP_069330428.1 / Number of copies: 12 / Enantiomer: LEVO
Source (natural)Organism: Rhodopseudomonas sphaeroides (bacteria)
Molecular weightTheoretical: 6.47378 KDa
SequenceString:
(FME)SKFYKIWMI FDPRRVFVAQ GVFLFLLAVM IHLILLSTPS YNWLEISAAK YNRV

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Macromolecule #5: Antenna pigment protein beta chain

MacromoleculeName: Antenna pigment protein beta chain / type: protein_or_peptide / ID: 5 / Number of copies: 14 / Enantiomer: LEVO
Source (natural)Organism: Rhodopseudomonas sphaeroides (bacteria)
Molecular weightTheoretical: 5.592361 KDa
SequenceString:
MADKSDLGYT GLTDEQAQEL HSVYMSGLWL FSAVAIVAHL AVYIWRPWF

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Macromolecule #6: Light-harvesting protein B-875 alpha chain

MacromoleculeName: Light-harvesting protein B-875 alpha chain / type: protein_or_peptide / ID: 6 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Rhodopseudomonas sphaeroides (bacteria)
Molecular weightTheoretical: 6.44577 KDa
SequenceString:
MSKFYKIWMI FDPRRVFVAQ GVFLFLLAVM IHLILLSTPS YNWLEISAAK YNRV

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Macromolecule #7: PufX

MacromoleculeName: PufX / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Rhodobacter sphaeroides (bacteria)
Molecular weightTheoretical: 9.01759 KDa
SequenceString:
MADKTIFNDH LNTNPKTNLR LWVAFQMMKG AGWAGGVFFG TLLLIGFFRV VGRMLPIDEN PAPAPNITGA LETGIELIKH LV

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Macromolecule #8: protein-U

MacromoleculeName: protein-U / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Rhodopseudomonas sphaeroides (bacteria)
Molecular weightTheoretical: 5.555558 KDa
SequenceString:
MPEVSEFAFR LMMAAVIFVG VGIMFAFAGG HWFVGLVVGG LVAAFFAATP NSN

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Macromolecule #9: BACTERIOCHLOROPHYLL A

MacromoleculeName: BACTERIOCHLOROPHYLL A / type: ligand / ID: 9 / Number of copies: 32 / Formula: BCL
Molecular weightTheoretical: 911.504 Da
Chemical component information

ChemComp-BCL:
BACTERIOCHLOROPHYLL A / Bacteriochlorophyll

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Macromolecule #10: BACTERIOPHEOPHYTIN A

MacromoleculeName: BACTERIOPHEOPHYTIN A / type: ligand / ID: 10 / Number of copies: 2 / Formula: BPH
Molecular weightTheoretical: 889.215 Da
Chemical component information

ChemComp-BPH:
BACTERIOPHEOPHYTIN A / Pheophytin

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Macromolecule #11: UBIQUINONE-10

MacromoleculeName: UBIQUINONE-10 / type: ligand / ID: 11 / Number of copies: 3 / Formula: U10
Molecular weightTheoretical: 863.343 Da
Chemical component information

ChemComp-U10:
UBIQUINONE-10 / Coenzyme Q10

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Macromolecule #12: (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-...

MacromoleculeName: (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE
type: ligand / ID: 12 / Number of copies: 13 / Formula: PGV
Molecular weightTheoretical: 749.007 Da
Chemical component information

ChemComp-PGV:
(1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE / phospholipid*YM / Phosphatidylglycerol

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Macromolecule #13: LAURYL DIMETHYLAMINE-N-OXIDE

MacromoleculeName: LAURYL DIMETHYLAMINE-N-OXIDE / type: ligand / ID: 13 / Number of copies: 6 / Formula: LDA
Molecular weightTheoretical: 229.402 Da
Chemical component information

ChemComp-LDA:
LAURYL DIMETHYLAMINE-N-OXIDE / LDAO, detergent*YM / Lauryldimethylamine oxide

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Macromolecule #14: FE (III) ION

MacromoleculeName: FE (III) ION / type: ligand / ID: 14 / Number of copies: 1 / Formula: FE
Molecular weightTheoretical: 55.845 Da

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Macromolecule #15: SPHEROIDENE

MacromoleculeName: SPHEROIDENE / type: ligand / ID: 15 / Number of copies: 27 / Formula: SPO
Molecular weightTheoretical: 568.914 Da
Chemical component information

ChemComp-7OT:
SPHEROIDENE

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Macromolecule #16: DODECYL-BETA-D-MALTOSIDE

MacromoleculeName: DODECYL-BETA-D-MALTOSIDE / type: ligand / ID: 16 / Number of copies: 24 / Formula: LMT
Molecular weightTheoretical: 510.615 Da
Chemical component information

ChemComp-LMT:
DODECYL-BETA-D-MALTOSIDE / detergent*YM

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Macromolecule #17: CARDIOLIPIN

MacromoleculeName: CARDIOLIPIN / type: ligand / ID: 17 / Number of copies: 4 / Formula: CDL
Molecular weightTheoretical: 1.464043 KDa
Chemical component information

ChemComp-CDL:
CARDIOLIPIN / phospholipid*YM / Cardiolipin

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration3.0 mg/mL
BufferpH: 8
GridMaterial: MOLYBDENUM
VitrificationCryogen name: ETHANE / Chamber humidity: 80 % / Chamber temperature: 277 K / Instrument: LEICA EM GP
DetailsThis sample was monodisperse.

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Detector mode: COUNTING / Average exposure time: 1.275 sec. / Average electron dose: 42.0 e/Å2
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 551846
CTF correctionSoftware - Name: CTFFIND
Initial angle assignmentType: NOT APPLICABLE
Final 3D classificationNumber classes: 4 / Avg.num./class: 160448 / Software - Name: RELION (ver. 3.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.94 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Number images used: 160448
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

5y5s

RefinementSpace: REAL / Protocol: RIGID BODY FIT / Overall B value: 60 / Target criteria: Correlation coefficient
Output model

PDB-7f0l:
STRUCTURE OF PHOTOSYNTHETIC LH1-RC SUPER-COMPLEX OF RHODOBACTER SPHAEROIDES MONOMER

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