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- EMDB-3531: Cryo-EM reconstruction of the large subunit of the chloroplast ri... -

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Entry
Database: EMDB / ID: 3531
TitleCryo-EM reconstruction of the large subunit of the chloroplast ribosome
SampleChloroplast 70S ribosome
SourceSpinacia oleracea / plant / spinach / ホウレンソウ
Map dataCryo-EM reconstruction of the 50S large subunit of the chloroplast ribosome
Methodsingle particle reconstruction, at 3.2 Å resolution
AuthorsBieri P / Leibundgut M
CitationEMBO J., 2017, 36, 475-486

EMBO J., 2017, 36, 475-486 StrPapers
The complete structure of the chloroplast 70S ribosome in complex with translation factor pY.
Philipp Bieri / Marc Leibundgut / Martin Saurer / Daniel Boehringer / Nenad Ban

Validation ReportPDB-ID: 5mmi

SummaryFull reportAbout validation report
DateDeposition: Dec 10, 2016 / Header (metadata) release: Jan 11, 2017 / Map release: Jan 11, 2017 / Last update: Dec 10, 2016

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.08
  • Imaged by UCSF CHIMERA
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  • Surface view colored by height
  • Surface level: 0.08
  • Imaged by UCSF CHIMERA
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  • Surface view with fitted model
  • Atomic models: : PDB-5mmi
  • Surface level: 0.08
  • Imaged by UCSF CHIMERA
  • Download
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Supplemental images

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Map

Fileemd_3531.map.gz (map file in CCP4 format, 131073 KB)
Projections & slices

Image control

Size
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
320 pix
1.39 Å/pix.
= 444.8 Å
320 pix
1.39 Å/pix.
= 444.8 Å
320 pix
1.39 Å/pix.
= 444.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Voxel sizeX=Y=Z: 1.39 Å
Density
Contour Level:0.08 (by author), 0.08 (movie #1):
Minimum - Maximum-0.2699295 - 0.6163046
Average (Standard dev.)0.0016259291 (0.0172451)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions320320320
Origin000
Limit319319319
Spacing320320320
CellA=B=C: 444.8 Å
α=β=γ: 90 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.391.391.39
M x/y/z320320320
origin x/y/z0.0000.0000.000
length x/y/z444.800444.800444.800
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS320320320
D min/max/mean-0.2700.6160.002

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Supplemental data

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Sample components

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Entire Chloroplast 70S ribosome

EntireName: Chloroplast 70S ribosome / Number of components: 38
MassTheoretical: 2.4 MDa

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Component #1: protein, Chloroplast 70S ribosome

ProteinName: Chloroplast 70S ribosome / Recombinant expression: No
MassTheoretical: 2.4 MDa
SourceSpecies: Spinacia oleracea / plant / spinach / ホウレンソウ
Source (natural)Organelle: chloroplast / Organ or tissue: leaf

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Component #2: protein, 50S ribosomal protein L31

ProteinName: 50S ribosomal protein L31 / Recombinant expression: No
MassTheoretical: 14.748201 kDa
SourceSpecies: Spinacia oleracea / plant / spinach / ホウレンソウ

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Component #3: protein, 50S ribosomal protein L32, chloroplastic

ProteinName: 50S ribosomal protein L32, chloroplastic / Recombinant expression: No
MassTheoretical: 6.650969 kDa
SourceSpecies: Spinacia oleracea / plant / spinach / ホウレンソウ

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Component #4: protein, 50S ribosomal protein L33, chloroplastic

ProteinName: 50S ribosomal protein L33, chloroplastic / Details: Zn-binding protein / Recombinant expression: No
MassTheoretical: 7.668121 kDa
SourceSpecies: Spinacia oleracea / plant / spinach / ホウレンソウ

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Component #5: protein, 50S ribosomal protein L34, chloroplastic

ProteinName: 50S ribosomal protein L34, chloroplastic / Recombinant expression: No
MassTheoretical: 16.126633 kDa
SourceSpecies: Spinacia oleracea / plant / spinach / ホウレンソウ

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Component #6: protein, 50S ribosomal protein L35, chloroplastic

ProteinName: 50S ribosomal protein L35, chloroplastic / Recombinant expression: No
MassTheoretical: 17.376322 kDa
SourceSpecies: Spinacia oleracea / plant / spinach / ホウレンソウ

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Component #7: protein, 50S ribosomal protein L36, chloroplastic

ProteinName: 50S ribosomal protein L36, chloroplastic / Details: Zn-binding protein / Recombinant expression: No
MassTheoretical: 4.414462 kDa
SourceSpecies: Spinacia oleracea / plant / spinach / ホウレンソウ

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Component #8: protein, plastid ribosomal protein cL37, PSRP5

ProteinName: plastid ribosomal protein cL37, PSRP5 / Recombinant expression: No
MassTheoretical: 15.694817 kDa
SourceSpecies: Spinacia oleracea / plant / spinach / ホウレンソウ

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Component #9: protein, 50S ribosomal protein 6, chloroplastic

ProteinName: 50S ribosomal protein 6, chloroplastic / Recombinant expression: No
MassTheoretical: 12.080688 kDa
SourceSpecies: Spinacia oleracea / plant / spinach / ホウレンソウ

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Component #10: nucleic-acid, 23S ribosomal RNA

Nucleic-acidName: 23S ribosomal RNA / Class: RNA / Structure: OTHER / Synthetic: No
Sequence:
UUCAAACGAG GAAAGGCUUA CGGUGGAUAC CUAGGCACCC AGAGACGAGG AAGGGCGUAU UAAUCGACGA AAUGCUUCGG GGAGUUGAAA AUAAGCAGAG AUCCGGAGAU UCCCGAAUAG GUCAACCUUU CGAACUUCUG CUGAAUCCAU GGGCAGGCAA GAGACAACCU GGCGAACUGA AACAUCUUAG UAGCCAGAGG AAAAGAAAGC AAAAGCGAUU CCCGUAGUAG CGGCGAGCGA AAUGGGAGCA GCCUAAACCG UGAAAACGGG GUUGUGGGAG AGCAAUACAA GCGUCGUGCU GCUAGGCGAA UCAGUGGAGU GCGGAACCCU AGAUGGUGAA AGUCCAGUAG CCGAAAGCAU CACUAGCUUA UGCUCUGACC CGAGUAGCAU GGGGCACGUG GAAUCCCGUG UGAAUCAGCA AGGACCACCU UGCAAGGCUA AAUACUCCUG GGUGACCGAU AGCGAAGUAG UACCGUGAGG GAAGGGUGAA AAGAACCCCC AUCGGGGAGU GAAAUAGAAC AUGAAACCGU AAGCUCUCAA GCAGUGGGAG GGGGACCAGA CCCUGACCGC GUGCCUGUUG AAGAAUGAGC CGGCGACUCA UAGGCAGUGG CUUGGUUAAG GGAACCCACC GGAGCCGUAG CGAAAGCGAG UCUUCAUAGG GCAAUUGUCA CUGCUUAUGG ACCCGAACCU GGGUGAUCUA UCCAUGACCA GGAUGAAGCU UGGGUGAAAC UAAGUGGAGG UCCGAACCGA CUGAUGUUGA AGAAUCAGCG GAUGAGUUGU GGUUAGGGGU GAAAUGCCAC UCGAACCCAG AGCUAGCUGG UUCUCCCCGA AAUGCGUUGA GGCGCAGCAG UUGACUGGAC AUCUAGGGGU AAAGCACUGU UUCGGUGCGG GCCGCGAGAG CGGUACCAAA UCGAGGCAAA CUCUGAAUAC UAGAUAUGAC CUCCAAAUAA CAGGGGUCAA GGUCGGCCAG UGAGACGAUG GGGGAUAAGC UUCAUCGUCG AGAGGGAAAC AGCCCGGAUC ACCAGCUAAG GCCCCUAAAU GACCGCUCAG UGAUAAAGGA GGUAGGGGUG CAGAGACAGC CAGGAGGUUU GCCUAGAAGC AGCCACCCUU GAAAGAGUGC GUAAUAGCUC ACUGAUCGAG CGCUCUUGCG CCGAAGAUGA ACGGGGCUAA GCGGUCUGCC GAAGCUGUGG GAUGUAAAAA AACAUCGGUA GGGGAGCGUU CCGUGUUAGG GAGAAACGCG UGCGUGAGCC GCGUUGGACG AAGCGGAAGC GAGAAUGUCG GCUUGAGUAA CGCAAACAUU GGUGAGAAUC CAAUGCCCCG AAAACCUAAG GGUUCCUCCG CAAGGUUCGU CCACGGAGGG UGAGUCAGGG CCUAAGAUCA GGCCGAAAGG CGUAGUCGAU GGACAACAGG UGAAUAUUCC UGUACUACCC CUUGUUGGUC CCGAGGGACG GAGGAGGCUA GGUUAGCCGA AAGAUGGUUA UCGGUUCAAG GACGCAAGGU GACCCUGUUU UUCAGGGUAA GAAGGGGUAG AGAAAAUGCC UCGAGCCAAU GUUCGAGUAC CAGGCGCUAC GGCGCUGAAG UAACCGAUGC CAUACUCCCA GGAAAAGCUC GAACGACCUU CAACAAAAGG GUACCUGUAC CCGAAACCGA CACAGGUAGG UAGGUAGAGA AUACCUAGGG GCGCGAGACA ACUCUCUCUA AGGAACUCGG CAAAAUAGCC CCGUAACUUC GGGAGAAGGG GUGCCCCCUC ACAAAGGGGG UCGAAGUGAC CAGGCCCGGG CGACUGUUUA CCAAAAACAC AGGUCUCCGC AAAGUCGUAA GACCAUGUAU GGGGGCUGAC GCCUGCCCAG UGCCGGAAGG UCAAGGAAGU UGGUGACCUG AUGACAGGGG AGCCGGCGAC CGAAGCCCCG GUGAACGGCG GCCGUAACUA UAACGGUCCU AAGGUAGCGA AAUUCCUUGU CGGGUAAGUU CCGACCCGCA CGAAAGGCGU AACGAUCUGG GCACUGUCUC GGAGAGAGGC UCGGUGAAAU AGACAUGUCU GUGAAGAUGC GGACUACCUG CACCUGGACA GAAAGACCCU AUGAAGCUUU ACUGUUCCCU GGGAUUGGCU UUGGGCUUUU CCUGCGCAGC UUAGGUGGAA GGCGAAGAAG GCCCCCUUCC GGGGGGGCCC GAGCCAUCAG UGAGAUACCA CUCUGGAAGA GCUAGAAUUC UAACCUUGUG UCAGGACCUA CGGGCCAAGG GACAUUCUCA GGUAGACAGU UUCUAUGGGG CGUAGGCCUC CCAAAAGGUA ACGGAGGCGU GCAAAGGUUU CCUCGGGCCG GACGGAGAUU GGCCCUCGAG UGCAAAGGCA GAAGGGAGCU UGACUGCAAG ACCCACCCGU CGAGCAGGGA CGAAAGUCGG CCUUAGUGAU CCGACGGUGC CGAGUGGAAG GGCCGUCGCU CAACGGAUAA AAGUUACUCU AGGGAUAACA GGCUGAUCUU CCCCAAGAGU UCACAUCGAC GGGAAGGUUU GGCACCUCGA UGUCGGCUCU UCGCCACCUG GGGCUGUAGU AUGUUCCAAG GGUUGGGCUG UUCGCCCAUU AAAGCGGUAC GUGAGCUGGG UUCAGAACGU CGUGAGACAG UUCGGUCCAU AUCCGGUGUG GGCGUUAGAG CAUUGAGAGG ACCUUUCCCU AGUACGAGAG GACCGGGAAG GACGCACCUC UGGUGUACCA GUUAUCGUGC CCACGGUAAA CGCUGGGUAG CCAAGUGCGG AGCGGAUAAC UGCUGAAAGC AUCUAAGUAG UAAGCCCACC CCAAGAUGAG UGCUCUCCUA
MassTheoretical: 911.34425 kDa
SourceSpecies: Spinacia oleracea / plant / spinach / ホウレンソウ

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Component #11: nucleic-acid, 5S ribosomal RNA

Nucleic-acidName: 5S ribosomal RNA / Class: RNA / Structure: OTHER / Synthetic: No
Sequence:
UAUUCUGGUG UCCUAGGCGU AGAGGAACCA CACCAAUCCA UCCCGAACUU GGUGGUUAAA CUCUACUGCG GUGACGAUAC UGUAGGGGAG GUCCUGCGGA AAAAUAGCUC GACGCCAGGA U
MassTheoretical: 39.014184 kDa
SourceSpecies: Spinacia oleracea / plant / spinach / ホウレンソウ

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Component #12: protein, 50S ribosomal protein L2, chloroplastic

ProteinName: 50S ribosomal protein L2, chloroplastic / Recombinant expression: No
MassTheoretical: 29.853623 kDa
SourceSpecies: Spinacia oleracea / plant / spinach / ホウレンソウ

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Component #13: protein, plastid ribosomal protein uL3c

ProteinName: plastid ribosomal protein uL3c / Recombinant expression: No
MassTheoretical: 33.03475 kDa
SourceSpecies: Spinacia oleracea / plant / spinach / ホウレンソウ

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Component #14: protein, plastid ribosomal protein uL4c

ProteinName: plastid ribosomal protein uL4c / Recombinant expression: No
MassTheoretical: 32.541645 kDa
SourceSpecies: Spinacia oleracea / plant / spinach / ホウレンソウ

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Component #15: protein, plastid ribosomal protein uL5c

ProteinName: plastid ribosomal protein uL5c
Details: Residues 39-52 were built as poly-alanine and deposited as UNK.
Recombinant expression: No
MassTheoretical: 28.182688 kDa
SourceSpecies: Spinacia oleracea / plant / spinach / ホウレンソウ

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Component #16: protein, plastid ribosomal protein uL6c

ProteinName: plastid ribosomal protein uL6c / Recombinant expression: No
MassTheoretical: 24.516748 kDa
SourceSpecies: Spinacia oleracea / plant / spinach / ホウレンソウ

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Component #17: protein, plastid ribosomal protein bL9c

ProteinName: plastid ribosomal protein bL9c / Recombinant expression: No
MassTheoretical: 22.038904 kDa
SourceSpecies: Spinacia oleracea / plant / spinach / ホウレンソウ

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Component #18: protein, plastid ribosomal protein uL10c

ProteinName: plastid ribosomal protein uL10c / Recombinant expression: No
MassTheoretical: 26.12823 kDa
SourceSpecies: Spinacia oleracea / plant / spinach / ホウレンソウ

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Component #19: protein, 50S ribosomal protein L11, chloroplastic

ProteinName: 50S ribosomal protein L11, chloroplastic / Recombinant expression: No
MassTheoretical: 23.68998 kDa
SourceSpecies: Spinacia oleracea / plant / spinach / ホウレンソウ

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Component #20: protein, 50S ribosomal protein L13, chloroplastic

ProteinName: 50S ribosomal protein L13, chloroplastic / Recombinant expression: No
MassTheoretical: 28.211629 kDa
SourceSpecies: Spinacia oleracea / plant / spinach / ホウレンソウ

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Component #21: protein, 50S ribosomal protein L14, chloroplastic

ProteinName: 50S ribosomal protein L14, chloroplastic / Recombinant expression: No
MassTheoretical: 13.484741 kDa
SourceSpecies: Spinacia oleracea / plant / spinach / ホウレンソウ

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Component #22: protein, plastid ribosomal protein uL15c

ProteinName: plastid ribosomal protein uL15c / Recombinant expression: No
MassTheoretical: 29.081514 kDa
SourceSpecies: Spinacia oleracea / plant / spinach / ホウレンソウ

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Component #23: protein, 50S ribosomal protein L16, chloroplastic

ProteinName: 50S ribosomal protein L16, chloroplastic / Recombinant expression: No
MassTheoretical: 15.328068 kDa
SourceSpecies: Spinacia oleracea / plant / spinach / ホウレンソウ

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Component #24: protein, plastid ribosomal protein bL17c

ProteinName: plastid ribosomal protein bL17c / Recombinant expression: No
MassTheoretical: 14.577172 kDa
SourceSpecies: Spinacia oleracea / plant / spinach / ホウレンソウ

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Component #25: protein, plastid ribosomal protein uL18c

ProteinName: plastid ribosomal protein uL18c / Recombinant expression: No
MassTheoretical: 18.410205 kDa
SourceSpecies: Spinacia oleracea / plant / spinach / ホウレンソウ

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Component #26: protein, 50S ribosomal protein L19, chloroplastic

ProteinName: 50S ribosomal protein L19, chloroplastic / Recombinant expression: No
MassTheoretical: 26.121254 kDa
SourceSpecies: Spinacia oleracea / plant / spinach / ホウレンソウ

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Component #27: protein, 50S ribosomal protein L20, chloroplastic

ProteinName: 50S ribosomal protein L20, chloroplastic / Recombinant expression: No
MassTheoretical: 15.725687 kDa
SourceSpecies: Spinacia oleracea / plant / spinach / ホウレンソウ

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Component #28: protein, 50S ribosomal protein L21, chloroplastic

ProteinName: 50S ribosomal protein L21, chloroplastic
Details: Residues 68-81 were built as poly-alanine and deposited as UNK.
Recombinant expression: No
MassTheoretical: 28.44173 kDa
SourceSpecies: Spinacia oleracea / plant / spinach / ホウレンソウ

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Component #29: protein, 50S ribosomal protein L22, chloroplastic

ProteinName: 50S ribosomal protein L22, chloroplastic / Recombinant expression: No
MassTheoretical: 23.292676 kDa
SourceSpecies: Spinacia oleracea / plant / spinach / ホウレンソウ

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Component #30: protein, 50S ribosomal protein L23, chloroplastic

ProteinName: 50S ribosomal protein L23, chloroplastic / Recombinant expression: No
MassTheoretical: 21.832164 kDa
SourceSpecies: Spinacia oleracea / plant / spinach / ホウレンソウ

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Component #31: protein, plastid ribosomal protein uL24c

ProteinName: plastid ribosomal protein uL24c / Recombinant expression: No
MassTheoretical: 21.417945 kDa
SourceSpecies: Spinacia oleracea / plant / spinach / ホウレンソウ

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Component #32: nucleic-acid, 4.5S ribosomal RNA

Nucleic-acidName: 4.5S ribosomal RNA / Class: RNA / Structure: OTHER / Synthetic: No
Sequence:
AGAGAAGGUC ACGGCGAGAC GAGCCGUUUA UCAUUACGAU AGGUGUCAAG UGGAAGUGCA GUGAUGUAUG CAGCUGAGGC AUCCUAACAG ACCCACAGAC UUGAAC
MassTheoretical: 34.334488 kDa
SourceSpecies: Spinacia oleracea / plant / spinach / ホウレンソウ

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Component #33: protein, plastid ribosomal protein bL27c

ProteinName: plastid ribosomal protein bL27c / Recombinant expression: No
MassTheoretical: 21.366447 kDa
SourceSpecies: Spinacia oleracea / plant / spinach / ホウレンソウ

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Component #34: protein, plastid ribosomal protein bL28c

ProteinName: plastid ribosomal protein bL28c / Recombinant expression: No
MassTheoretical: 16.460488 kDa
SourceSpecies: Spinacia oleracea / plant / spinach / ホウレンソウ

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Component #35: protein, plastid ribosomal protein uL29c

ProteinName: plastid ribosomal protein uL29c / Recombinant expression: No
MassTheoretical: 19.083385 kDa
SourceSpecies: Spinacia oleracea / plant / spinach / ホウレンソウ

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Component #36: nucleic-acid, E-site tRNA

Nucleic-acidName: E-site tRNA / Class: RNA / Details: CA-3' end of E-site tRNA / Structure: OTHER / Synthetic: No
Sequence:
CA
MassTheoretical: 0.58943 kDa
SourceSpecies: Spinacia oleracea / plant / spinach / ホウレンソウ

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Component #37: ligand, ZINC ION

LigandName: ZINC ION / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 6.540905 MDa

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Component #38: ligand, MAGNESIUM ION

LigandName: MAGNESIUM ION / Number of Copies: 501 / Recombinant expression: No
MassTheoretical: 2.430505 MDa

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Experimental details

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Sample preparation

Specimen stateparticle
Sample solutionSpecimen conc.: 0.12 mg/ml / pH: 7.6
VitrificationInstrument: FEI VITROBOT MARK I / Cryogen name: ETHANE-PROPANE MIXTURE / Temperature: 278 K / Humidity: 100 %

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 20 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 59000 X (nominal) / Cs: 2.7 mm / Imaging mode: BRIGHT FIELD / Defocus: 800 - 3500 nm
Specimen HolderModel: FEI TITAN KRIOS AUTOGRID HOLDER
CameraDetector: FEI FALCON II (4k x 4k)

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Image acquisition

Image acquisitionNumber of digital images: 2796

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C1 (asymmetric) / Number of projections: 154332
3D reconstructionSoftware: RELION / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF
FSC plot (resolution assessment)

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Atomic model buiding

Output model

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