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- EMDB-48835: Cryo-EM structure of an extended F. johnsoniae BAM complex, compo... -

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Basic information

Entry
Database: EMDB / ID: EMD-48835
TitleCryo-EM structure of an extended F. johnsoniae BAM complex, composite map
Map datacomposite map
Sample
  • Complex: BAM complex
    • Protein or peptide: x 5 types
  • Protein or peptide: x 1 types
  • Ligand: x 7 types
KeywordsBAM complex / BamA / BamD / BamF / BamG / BamM / BamP / outer-membrane proteins / OMP / MEMBRANE PROTEIN
Function / homology
Function and homology information


membrane assembly / peptidyl-prolyl cis-trans isomerase activity / cell outer membrane / calcium ion binding
Similarity search - Function
Protein of unknown function DUF4270 / Domain of unknown function (DUF4270) / TSP type-3 repeat / Outer membrane protein assembly factor BamD / Outer membrane lipoprotein BamD-like / Outer membrane lipoprotein / Outer membrane protein assembly factor BamA / POTRA domain, BamA/TamA-like / Surface antigen variable number repeat / POTRA domain ...Protein of unknown function DUF4270 / Domain of unknown function (DUF4270) / TSP type-3 repeat / Outer membrane protein assembly factor BamD / Outer membrane lipoprotein BamD-like / Outer membrane lipoprotein / Outer membrane protein assembly factor BamA / POTRA domain, BamA/TamA-like / Surface antigen variable number repeat / POTRA domain / POTRA domain profile. / Bacterial surface antigen (D15) / Omp85 superfamily domain / Peptidyl-prolyl cis-trans isomerase domain superfamily / Prokaryotic membrane lipoprotein lipid attachment site profile. / Tetratricopeptide-like helical domain superfamily
Similarity search - Domain/homology
DNA uptake lipoprotein-like protein / CarboxypepD_reg-like domain-containing protein / Surface antigen (D15) / Long-chain fatty acid transport protein / Hypothetical lipoprotein / Hypothetical lipoprotein
Similarity search - Component
Biological speciesFlavobacterium johnsoniae UW101 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.7 Å
AuthorsDeme JC / Lea SM
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)CCR Core Funding for Lea Group United States
CitationJournal: To Be Published
Title: An extended BAM complex in the Bacteroidota
Authors: Liu X / Orenday Tapia L / Deme JC / Lea SM / Berks BC
History
DepositionJan 28, 2025-
Header (metadata) releaseJul 9, 2025-
Map releaseJul 9, 2025-
UpdateJul 9, 2025-
Current statusJul 9, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_48835.png

Downloads & links

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Map

FileDownload / File: emd_48835.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationcomposite map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.73 Å/pix.
x 512 pix.
= 374.784 Å		0.73 Å/pix.
x 512 pix.
= 374.784 Å		0.73 Å/pix.
x 512 pix.
= 374.784 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.732 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 2.75
Minimum - Maximum-1.2069323 - 16.665247000000001
Average (Standard dev.)0.11432439 (±0.38223737)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 374.784 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : BAM complex

EntireName: BAM complex
Components
  • Complex: BAM complex
    • Protein or peptide: DNA uptake lipoprotein-like protein
    • Protein or peptide: Surface antigen (D15)
    • Protein or peptide: Hypothetical lipoprotein
    • Protein or peptide: Hypothetical lipoprotein
    • Protein or peptide: CarboxypepD_reg-like domain-containing protein
  • Protein or peptide: Long-chain fatty acid transport protein
  • Ligand: DIACYL GLYCEROL
  • Ligand: (2~{R},4~{R},5~{R},6~{R})-6-[(1~{R})-1,2-bis(oxidanyl)ethyl]-2-[(2~{R},4~{R},5~{R},6~{R})-6-[(1~{R})-1,2-bis(oxidanyl)ethyl]-5-[(2~{S},3~{S},4~{R},5~{R},6~{R})-6-[(1~{S})-1,2-bis(oxidanyl)ethyl]-4-[(2~{R},3~{S},4~{R},5~{S},6~{R})-6-[(1~{S})-2-[(2~{S},3~{S},4~{S},5~{S},6~{R})-6-[(1~{S})-1,2-bis(oxidanyl)ethyl]-3,4,5-tris(oxidanyl)oxan-2-yl]oxy-1-oxidanyl-ethyl]-3,4-bis(oxidanyl)-5-phosphonooxy-oxan-2-yl]oxy-3-oxidanyl-5-phosphonooxy-oxan-2-yl]oxy-2-carboxy-2-[[(2~{R},3~{S},4~{R},5~{R},6~{R})-5-[[(3~{R})-3-dodecanoyloxytetradecanoyl]amino]-6-[[(2~{R},3~{S},4~{R},5~{R},6~{R})-3-oxidanyl-5-[[(3~{R})-3-oxidanyltetradecanoyl]amino]-4-[(3~{R})-3-oxidanyltetradecanoyl]oxy-6-phosphonooxy-oxan-2-yl]methoxy]-3-phosphonooxy-4-[(3~{R})-3-tetradecanoyloxytetradecanoyl]oxy-oxan-2-yl]methoxy]oxan-4-yl]oxy-4,5-bis(oxidanyl)oxane-2-carboxylic acid
  • Ligand: PHOSPHATIDYLETHANOLAMINE
  • Ligand: alpha-D-mannopyranose
  • Ligand: PALMITIC ACID
  • Ligand: CALCIUM ION
  • Ligand: water

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Supramolecule #1: BAM complex

SupramoleculeName: BAM complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3, #5-#6
Source (natural)Organism: Flavobacterium johnsoniae UW101 (bacteria)

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Macromolecule #1: DNA uptake lipoprotein-like protein

MacromoleculeName: DNA uptake lipoprotein-like protein / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Flavobacterium johnsoniae UW101 (bacteria)
Molecular weightTheoretical: 30.219377 KDa
SequenceString: MKKIVSLLIV AALFCSCSEY QKALKNEDVA AKFEVATKMY DAGKYNKAIR LFEQLAPTYR GKPQAEKLFY MFSQSYYKTK QYYLAGYQF ESFVSGYPRS EKVQEAAFLG AYSYSKLAPV YSLDQADTVK ALDKLQAFID NYPNSEYLAQ ANESVKILNG K LEKKAYEN ...String:
MKKIVSLLIV AALFCSCSEY QKALKNEDVA AKFEVATKMY DAGKYNKAIR LFEQLAPTYR GKPQAEKLFY MFSQSYYKTK QYYLAGYQF ESFVSGYPRS EKVQEAAFLG AYSYSKLAPV YSLDQADTVK ALDKLQAFID NYPNSEYLAQ ANESVKILNG K LEKKAYEN AKGYNTISDY KSALVAFDNF IADFPGTPLK EDALFYKYDS AYQLAINSVP SKMEERLHVA QTAYANLMKY KS DTKYKEK ADQMNARVET DLQKFTK

UniProtKB: DNA uptake lipoprotein-like protein

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Macromolecule #2: Surface antigen (D15)

MacromoleculeName: Surface antigen (D15) / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Flavobacterium johnsoniae UW101 (bacteria)
Molecular weightTheoretical: 101.49032 KDa
SequenceString: MLQKRIPQII CTLLLLGSFS QIKAQDRVPF DQGKKYTLAK VSVVGKISFN EQTVVTFSGL QKGQEITVPG EEITSAIKKL GKLGLFDEI AFYINKVEND SIYLDLNIVE LPKLNEVKIT GVKKSKVEGL IKDNNLTKNK IVNENLITTT KNYIENKYKK D GFYNTKVV ...String:
MLQKRIPQII CTLLLLGSFS QIKAQDRVPF DQGKKYTLAK VSVVGKISFN EQTVVTFSGL QKGQEITVPG EEITSAIKKL GKLGLFDEI AFYINKVEND SIYLDLNIVE LPKLNEVKIT GVKKSKVEGL IKDNNLTKNK IVNENLITTT KNYIENKYKK D GFYNTKVV ITTTPDTTAG NQVNMLVRVD KGDKVKISSI DFTGNKQLSD SKLRAAMKDT KQKNVLRVFK ASKFIPEKYK TD LEKVIAS YKEKGYRDAR IIYDSVIYNK KKNMLAIKID VEEGNKYYFG NIKFLGNTVY SDQQLNRYLG IKKGETYNGV LLE KRIADN TKPDGEDITN LYQNNGYLFS KINAVEVKTV NDTIDFEIRI TEGPIAYFNK IYVTGNDKTN DHVIYRELRT KPGN KYSKE ELVRTIREIG QLGFFDPESI KPEFRNVDPA AGTVDIEYQL VEKGSSQVEL QGGYGGGGFI GTLGLSFNNF SARKL FDKD AYKPLPMGDG QKVALRLQGS TYFQTYSLSF SEPWFGGKKP VQFSSSISYS KQFNYNYSSR DVNRNQSFNI FTVQVG LAK RLTVPDDYFV LSQSVSYQHY DLNNYYTGLF TFGNGASRNL AYTIGLSRSN KGVNPIFPTY GSEFSISAKV TPPYSLF NN INYGDLQNQK EYKTQYTGTT TTTGIDGQAI NPGDYTKTET VNGQSGTVSV GSDYKSADTD VGKVDQKKYN WLEYYKVK F KADWYTKIYG KLVLRTLTEF GFLGAYDQSR GVVPFERFYL GGDGMANYSM DGRETIQLRG YPNNSLTPII EDRNSSRYG QQIGATIYNK FSMELRYPIT LKSSASIYAL TFLEAGSSYP TFKDYNPFDL NRSAGAGLRV FMPAFGLLGI DFGYGFDALP GSTTNKANG WETHFIIGQQ F

UniProtKB: Surface antigen (D15)

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Macromolecule #3: Hypothetical lipoprotein

MacromoleculeName: Hypothetical lipoprotein / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Flavobacterium johnsoniae UW101 (bacteria)
Molecular weightTheoretical: 57.094242 KDa
SequenceString: CDKDFNAIGG DLIGDDHFGL ESEKYDVLSY NQEVTSVQSN VLPTSALGIY SNPVFGETTA NYVTQVALVA YAPSIGEDPV IESAVLSIP YFSHVTANNT DGSHTYELDS IYGPANGKLK LSVYESGYQM RSSFPSNGTE LPQYYYTSQN STFDQAKVGT R LNDDLTKP ...String:
CDKDFNAIGG DLIGDDHFGL ESEKYDVLSY NQEVTSVQSN VLPTSALGIY SNPVFGETTA NYVTQVALVA YAPSIGEDPV IESAVLSIP YFSHVTANNT DGSHTYELDS IYGPANGKLK LSVYESGYQM RSSFPSNGTE LPQYYYTSQN STFDQAKVGT R LNDDLTKP FQNDQFFFSS EEYKTVTKDS NDKETTTYTA PEMRLNLNSA FFQDKILKAP ASKIASTDVF QEYFRGLYFK VE KADGSPS NMALMDFSKG KITITYKAKT DITTDAPETT EERTIVINLV NPTSSGGTAN LLQDAKSAGY SGAISSSNVN KTE GDERLY IKGGQGSAAV IKLNDFASKL DDIRAKNWKV NEANLIFNID SDLMTGADEP KRVYLYDLTN NVPLADYYAD QTTS LTVGD TKGAKYVFGG LINLGDNKRG KTYKIRITEY IRNLIKDKTA KNVNLGLVVT ESIGITTSNF LENRIVLQPN EYFSQ VPRA SIMNPLGTIL YGGKASVPDD KRLRLEVYYT KPN

UniProtKB: Hypothetical lipoprotein

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Macromolecule #4: Long-chain fatty acid transport protein

MacromoleculeName: Long-chain fatty acid transport protein / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Flavobacterium johnsoniae UW101 (bacteria)
Molecular weightTheoretical: 44.45898 KDa
SequenceString: MIKKIIISAC LLISFVSFAQ QGTASPYSFY GIGDIKFKGT LEYRSMAGVA VEQDSIHLNI ENPASYASLM QTTFTVGGTF GTSTLKSNT GSAKAQRTTF DYLAVGIPVG KFGVSFGLIP LSSVGYKILD DNTATEGAVS SQLSGKGGIN KVYFGVGYKI K PHWTIGAD ...String:
MIKKIIISAC LLISFVSFAQ QGTASPYSFY GIGDIKFKGT LEYRSMAGVA VEQDSIHLNI ENPASYASLM QTTFTVGGTF GTSTLKSNT GSAKAQRTTF DYLAVGIPVG KFGVSFGLIP LSSVGYKILD DNTATEGAVS SQLSGKGGIN KVYFGVGYKI K PHWTIGAD VQYNFGKITT TSIEQVTGVQ NGTSESNAST LSGANFDLGT MYQTKIYKKV NLFTSLSYTF SSNLNSENVR EI NVSGDPD PYAYPASTTK LKLPSRVIIG AGIGESRKWL VGTTLAFQGE GQLTNYYNAM DNVRYENYAK YAIGGYYIPN YTS FTSYLS RITYRAGLKY EKIGLIVNNE SIKDVGMTLG AGIPIPGYFS NVNIGIEFGK KGTVSSNLVQ ENYVNFSVGF SFND KWFVK SKFN

UniProtKB: Long-chain fatty acid transport protein

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Macromolecule #5: Hypothetical lipoprotein

MacromoleculeName: Hypothetical lipoprotein / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Flavobacterium johnsoniae UW101 (bacteria)
Molecular weightTheoretical: 43.899273 KDa
SequenceString: MNKFKYYFVL LLAGLAIVSC NKKDDDEEIV PLRDYQEQYN TDNANIEEYL NTYFITVTDA PGEQTDQDVT FTKITDPSTQ PSIMSYLNS PTFPKLLKRE VPMHGIVYQM YYLVLREGTG TSPMNTDGAF TSYRGEYLTR VAKTDTEAEH LSTTFFEQVL F PTKALDLY ...String:
MNKFKYYFVL LLAGLAIVSC NKKDDDEEIV PLRDYQEQYN TDNANIEEYL NTYFITVTDA PGEQTDQDVT FTKITDPSTQ PSIMSYLNS PTFPKLLKRE VPMHGIVYQM YYLVLREGTG TSPMNTDGAF TSYRGEYLTR VAKTDTEAEH LSTTFFEQVL F PTKALDLY GTIIGWSEAF PQFKTGTATM KPDGSMKYEN FGAGVLFIPS GLGYYGSGAS AIPAYSPLIF SIKLYDLTRL DH DLDGVFD FEEDINGDGY VYDFRNTTEY PTPPANQYDD DTDKDGIADF LDSDDDGDGY STLFEITKPT GTEFLGGLSK YYP YNPVSD NPATPNYDET EKYGIPRRPT GELTNPNLPE SINNPRKFIE DDYLAAGRKR IHLDNTYPYK KN

UniProtKB: Hypothetical lipoprotein

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Macromolecule #6: CarboxypepD_reg-like domain-containing protein

MacromoleculeName: CarboxypepD_reg-like domain-containing protein / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Flavobacterium johnsoniae UW101 (bacteria)
Molecular weightTheoretical: 28.413742 KDa
SequenceString: MKNKLGVFVV CLFCQIMLGQ NGTRKSLHGQ VTNKSLAIES GYVMNINAKS RTFIGPGGLF DILAQPKDTL LFTGIAFQSK KIVLTEKDC SQILFSVSLD LVSNELKEVL VRKDLKVKSL DSNTQKYVDM QFEDDRQSTA KNTVMYSDQT IKYGTDFVRI F KDVKKLLS ...String:
MKNKLGVFVV CLFCQIMLGQ NGTRKSLHGQ VTNKSLAIES GYVMNINAKS RTFIGPGGLF DILAQPKDTL LFTGIAFQSK KIVLTEKDC SQILFSVSLD LVSNELKEVL VRKDLKVKSL DSNTQKYVDM QFEDDRQSTA KNTVMYSDQT IKYGTDFVRI F KDVKKLLS KNNEKEEVIS DIAFVEYSKA NFKPDFYTKT LGLKPDEVDL FLMFCSNDPE SKRHLNEDQK FELIDFLINK NA EFKKVNA AQ

UniProtKB: CarboxypepD_reg-like domain-containing protein

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Macromolecule #9: DIACYL GLYCEROL

MacromoleculeName: DIACYL GLYCEROL / type: ligand / ID: 9 / Number of copies: 1 / Formula: DGA
Molecular weightTheoretical: 625.018 Da
Chemical component information

ChemComp-DGA:
DIACYL GLYCEROL

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Macromolecule #10: (2~{R},4~{R},5~{R},6~{R})-6-[(1~{R})-1,2-bis(oxidanyl)ethyl]-2-[(...

MacromoleculeName: (2~{R},4~{R},5~{R},6~{R})-6-[(1~{R})-1,2-bis(oxidanyl)ethyl]-2-[(2~{R},4~{R},5~{R},6~{R})-6-[(1~{R})-1,2-bis(oxidanyl)ethyl]-5-[(2~{S},3~{S},4~{R},5~{R},6~{R})-6-[(1~{S})-1,2-bis(oxidanyl)ethyl] ...Name: (2~{R},4~{R},5~{R},6~{R})-6-[(1~{R})-1,2-bis(oxidanyl)ethyl]-2-[(2~{R},4~{R},5~{R},6~{R})-6-[(1~{R})-1,2-bis(oxidanyl)ethyl]-5-[(2~{S},3~{S},4~{R},5~{R},6~{R})-6-[(1~{S})-1,2-bis(oxidanyl)ethyl]-4-[(2~{R},3~{S},4~{R},5~{S},6~{R})-6-[(1~{S})-2-[(2~{S},3~{S},4~{S},5~{S},6~{R})-6-[(1~{S})-1,2-bis(oxidanyl)ethyl]-3,4,5-tris(oxidanyl)oxan-2-yl]oxy-1-oxidanyl-ethyl]-3,4-bis(oxidanyl)-5-phosphonooxy-oxan-2-yl]oxy-3-oxidanyl-5-phosphonooxy-oxan-2-yl]oxy-2-carboxy-2-[[(2~{R},3~{S},4~{R},5~{R},6~{R})-5-[[(3~{R})-3-dodecanoyloxytetradecanoyl]amino]-6-[[(2~{R},3~{S},4~{R},5~{R},6~{R})-3-oxidanyl-5-[[(3~{R})-3-oxidanyltetradecanoyl]amino]-4-[(3~{R})-3-oxidanyltetradecanoyl]oxy-6-phosphonooxy-oxan-2-yl]methoxy]-3-phosphonooxy-4-[(3~{R})-3-tetradecanoyloxytetradecanoyl]oxy-oxan-2-yl]methoxy]oxan-4-yl]oxy-4,5-bis(oxidanyl)oxane-2-carboxylic acid
type: ligand / ID: 10 / Number of copies: 1 / Formula: JSG
Molecular weightTheoretical: 2.975178 KDa
Chemical component information

ChemComp-JSG:
(2~{R},4~{R},5~{R},6~{R})-6-[(1~{R})-1,2-bis(oxidanyl)ethyl]-2-[(2~{R},4~{R},5~{R},6~{R})-6-[(1~{R})-1,2-bis(oxidanyl)ethyl]-5-[(2~{S},3~{S},4~{R},5~{R},6~{R})-6-[(1~{S})-1,2-bis(oxidanyl)ethyl]-4-[(2~{R},3~{S},4~{R},5~{S},6~{R})-6-[(1~{S})-2-[(2~{S},3~{S},4~{S},5~{S},6~{R})-6-[(1~{S})-1,2-bis(oxidanyl)ethyl]-3,4,5-tris(oxidanyl)oxan-2-yl]oxy-1-oxidanyl-ethyl]-3,4-bis(oxidanyl)-5-phosphonooxy-oxan-2-yl]oxy-3-oxidanyl-5-phosphonooxy-oxan-2-yl]oxy-2-carboxy-2-[[(2~{R},3~{S},4~{R},5~{R},6~{R})-5-[[(3~{R})-3-dodecanoyloxytetradecanoyl]amino]-6-[[(2~{R},3~{S},4~{R},5~{R},6~{R})-3-oxidanyl-5-[[(3~{R})-3-oxidanyltetradecanoyl]amino]-4-[(3~{R})-3-oxidanyltetradecanoyl]oxy-6-phosphonooxy-oxan-2-yl]methoxy]-3-phosphonooxy-4-[(3~{R})-3-tetradecanoyloxytetradecanoyl]oxy-oxan-2-yl]methoxy]oxan-4-yl]oxy-4,5-bis(oxidanyl)oxane-2-carboxylic acid

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Macromolecule #11: PHOSPHATIDYLETHANOLAMINE

MacromoleculeName: PHOSPHATIDYLETHANOLAMINE / type: ligand / ID: 11 / Number of copies: 2 / Formula: PTY
Molecular weightTheoretical: 734.039 Da
Chemical component information

ChemComp-PTY:
PHOSPHATIDYLETHANOLAMINE / phospholipid*YM

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Macromolecule #12: alpha-D-mannopyranose

MacromoleculeName: alpha-D-mannopyranose / type: ligand / ID: 12 / Number of copies: 1 / Formula: MAN
Molecular weightTheoretical: 180.156 Da
Chemical component information

ChemComp-MAN:
alpha-D-mannopyranose

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Macromolecule #13: PALMITIC ACID

MacromoleculeName: PALMITIC ACID / type: ligand / ID: 13 / Number of copies: 1 / Formula: PLM
Molecular weightTheoretical: 256.424 Da
Chemical component information

ChemComp-PLM:
PALMITIC ACID

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Macromolecule #14: CALCIUM ION

MacromoleculeName: CALCIUM ION / type: ligand / ID: 14 / Number of copies: 7 / Formula: CA
Molecular weightTheoretical: 40.078 Da

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Macromolecule #15: water

MacromoleculeName: water / type: ligand / ID: 15 / Number of copies: 16 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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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

BufferpH: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: TFS FALCON 4i (4k x 4k) / Average electron dose: 60.3 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.7 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 55796
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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