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- EMDB-48371: Xenorhabdus nematophilus XptA2 State 2, 1181insYWK1183, D1182T mutant -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-48371
TitleXenorhabdus nematophilus XptA2 State 2, 1181insYWK1183, D1182T mutant
Map dataXenorhabdus nematophilus XptA2 State 2, 1181insYWK1183, D1182T mutant
Sample
  • Complex: A subunit of the Xenorhabdus nematophilus ABC Toxin Complex
    • Protein or peptide: XptA2 protein
KeywordsTcA / Pore Forming Toxin / TOXIN
Function / homology
Function and homology information


: / TcdA1, receptor binding domain / ABC toxin, N-terminal domain / ABC toxin N-terminal region / TcA receptor binding domain / TcA receptor binding domain / Insecticidal toxin complex/plasmid virulence protein / Tc toxin complex TcA, C-terminal TcB-binding domain / Neuraminidase-like domain / Salmonella virulence plasmid 28.1kDa A protein ...: / TcdA1, receptor binding domain / ABC toxin, N-terminal domain / ABC toxin N-terminal region / TcA receptor binding domain / TcA receptor binding domain / Insecticidal toxin complex/plasmid virulence protein / Tc toxin complex TcA, C-terminal TcB-binding domain / Neuraminidase-like domain / Salmonella virulence plasmid 28.1kDa A protein / Tc toxin complex TcA C-terminal TcB-binding domain / Neuraminidase-like domain
Similarity search - Domain/homology
Biological speciesXenorhabdus nematophila (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.3 Å
AuthorsAller SG / Martin CL
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)P01HL128203 United States
CitationJournal: To Be Published
Title: Xenorhabdus nematophilus XptA2 State 2, YWKT mutant
Authors: Aller SG / Martin CL / Hill JH / Wright BD / Fernandez SR / Lapi SE / Miller AL / Yoon KJ
History
DepositionDec 19, 2024-
Header (metadata) releaseJan 15, 2025-
Map releaseJan 15, 2025-
UpdateJan 15, 2025-
Current statusJan 15, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_48371.png

Downloads & links

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Map

FileDownload / File: emd_48371.map.gz / Format: CCP4 / Size: 56.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationXenorhabdus nematophilus XptA2 State 2, 1181insYWK1183, D1182T mutant
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.93 Å/pix.
x 246 pix.
= 473.796 Å		1.93 Å/pix.
x 246 pix.
= 473.796 Å		1.93 Å/pix.
x 246 pix.
= 473.796 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.926 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.29
Minimum - Maximum-0.4697369 - 1.0689932
Average (Standard dev.)0.000100346966 (±0.056194562)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions246246246
Spacing246246246
CellA=B=C: 473.796 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half Map B

Fileemd_48371_half_map_1.map
AnnotationHalf Map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half Map A

Fileemd_48371_half_map_2.map
AnnotationHalf Map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : A subunit of the Xenorhabdus nematophilus ABC Toxin Complex

EntireName: A subunit of the Xenorhabdus nematophilus ABC Toxin Complex
Components
  • Complex: A subunit of the Xenorhabdus nematophilus ABC Toxin Complex
    • Protein or peptide: XptA2 protein

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Supramolecule #1: A subunit of the Xenorhabdus nematophilus ABC Toxin Complex

SupramoleculeName: A subunit of the Xenorhabdus nematophilus ABC Toxin Complex
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Xenorhabdus nematophila (bacteria)

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Macromolecule #1: XptA2 protein

MacromoleculeName: XptA2 protein / type: protein_or_peptide / ID: 1 / Number of copies: 5 / Enantiomer: LEVO
Source (natural)Organism: Xenorhabdus nematophila (bacteria)
Molecular weightTheoretical: 284.769688 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MYSTAVLLNK ISPTRDGQTM TLADLQYLSF SELRKIFDDQ LSWGEARHLY HETIEQKKNN RLLEARIFTR ANPQLSGAIR LGIERDSVS RSYDEMFGAR SSSFVKPGSV ASMFSPAGYL TELYREAKDL HFSSSAYHLD NRRPDLADLT LSQSNMDTEI S TLTLSNEL ...String:
MYSTAVLLNK ISPTRDGQTM TLADLQYLSF SELRKIFDDQ LSWGEARHLY HETIEQKKNN RLLEARIFTR ANPQLSGAIR LGIERDSVS RSYDEMFGAR SSSFVKPGSV ASMFSPAGYL TELYREAKDL HFSSSAYHLD NRRPDLADLT LSQSNMDTEI S TLTLSNEL LLEHITRKTG GDSDALMESL STYRQAIDTP YHQPYETIRQ VIMTHDSTLS ALSRNPEVMG QAEGASLLAI LA NISPELY NILTEEITEK NADALFAQNF SENITPENFA SQSWIAKYYG LELSEVQKYL GMLQNGYSDS TSAYVDNIST GLV VNNESK LEAYKITRVK TDDYDKNINY FDLMYEGNNQ FFIRANFKVS REFGATLRKN AGPSGIVGSL SGPLIANTNF KSNY LSNIS DSEYKNGVKI YAYRYTSSTS ATNQGGGIFT FESYPLTIFA LKLNKAIRLC LTSGLSPNEL QTIVRSDNAQ GIIND SVLT KVFYTLFYSH RYALSFDDAQ VLNGSVINQY ADDDSVSHFN RLFNTPPLKG KIFEADGNTV SIDPDEEQST FARSAL MRG LGVNSGELYQ LGKLAGVLDA QNTITLSVFV ISSLYRLTLL ARVHQLTVNE LCMLYGLSPF NGKTTASLSS GELPRLV IW LYQVTQWLTE AEITTEAIWL LCTPEFSGNI SPEISNLLNN LRPSISEDMA QSHNRELQAE ILAPFIAATL HLASPDMA R YILLWTDNLR PGGLDIAGFM TLVLKESLNA NETTQLVQFC HVMAQLSLSV QTLRLSEAEL SVLVISGFAV LGAKNQPAG QHNIDTLFSL YRFHQWINGL GNPGSDTLDM LRQQTLTADR LASVMGLDIS MVTQAMVSAG VNQLQCWQDI NTVLQWIDVA SALHTMPSV IRTLVNIRYV TALNKAESNL PSWDEWQTLA ENMEAGLSTQ QAQTLADYTA ERLSSVLCNW FLANIQPEGV S LHSRDDLY SYFLIDNQVS SAIKTTRLAE AIAGIQLYIN RALNRIEPNA RADVSTRQFF TDWTVNNRYS TWGGVSRLVY YP ENYIDPT QRIGQTRMMD ELLENISQSK LSRDTVEDAF KTYLTRFETV ADLKVVSAYH DNVNSNTGLT WFVGQTRENL PEY YWRNVD ISRMQAGELA ANAWKEWTKI DTAVNPYKDA IRPVIFRERL HLIWVEKEEV AKNGTYWKTP VETYDRFTLK LAFL RHDGS WSAPWSYDIT TQVEAVTDKK PDTERLALAA SGFQGEDTLL VFVYKTGKSY SDFGGSNKNV AGMTIYGDGS FKKME NTAL SRYSQLKNTF DIIHTQGNDL VRKASYRFAQ DFEVPASLNM GSAIGDDSLT VMENGNIPQI TSKYSSDNLA ITLHNA AFT VRYDGSGNVI RNKQISAMKL TGVDGKSQYG NAFIIANTVK HYGGYSDLGG PITVYNKTKN YIASVQGHLM NADYTRR LI LTPVENNYYA RLFEFPFSPN TILNTVFTVG SNKTSDFKKC SYAVDGNNSQ GFQIFSSYQS SGWLDIDTGI NNTDIKIT V MAGSKTHTFT ASDHIASLPA NSFDAMPYTF KPLEIDASSL AFTNNIAPLD IVFETKAKDG RVLGKIKQTL SVKRVNYNP EDILFLRETH SGAQYMQLGV YRIRLNTLLA SQLVSRANTG IDTILTMETQ RLPEPPLGEG FFANFVLPKY DPAEHGDERW FKIHIGNVG GNTGRQPYYS GMLSDTSETS MTLFVPYAEG YYMHEGVRLG VGYQKITYDN TWESAFFYFD ETKQQFVLIN D ADHDSGMT QQGIVKNIKK YKGFLNVSIA TGYSAPMDFN SASALYYWEL FYYTPMMCFQ RLLQEKQFDE ATQWINYVYN PA GYIVNGE IAPWIWNCRP LEETTSWNAN PLDAIDPDAV AQNDPMHYKI ATFMRLLDQL ILRGDMAYRE LTRDALNEAK MWY VRTLEL LGDEPEDYGS QQWAAPSLSG AASQTVQAAY QQDLTMLGRG GVSKNLRTAN SLVGLFLPEY NPALTDYWQT LRLR LFNLR HNLSIDGQPL SLAIYAEPTD PKALLTSMVQ ASQGGSAVLP GTLSLYRFPV MLERTRNLVA QLTQFGTSLL SMAEH DDAD ELTTLLLQQG MELATQSIRI QQRTVDEVDA DIAVLAESRR SAQNRLEKYQ QLYDEDINHG EQRAMSLLDA AAGQSL AGQ VLSIAEGVAD LVPNVFGLAC GGSRWGAALR ASASVMSLSA TASQYSADKI SRSEAYRRRR QEWEIQRDNA DGEVKQM DA QLESLKIRRE AAQMQVEYQE TQQAHTQAQL ELLQRKFTNK ALYSWMRGKL SAIYYQFFDL TQSFCLMAQE ALRRELTD N GVTFIRGGAW NGTTAGLMAG ETLLLNLAEM EKVWLERDER ALEVTRTVSL AQFYQALSSD NFNLTEKLTQ FLREGKGNV GASGNELKLS NRQIEASVRL SDLKIFSDYP ESLGNTRQLK QVSVTLPALV GPYEDIRAVL NYGGSIVMPR GCSAIALSHG VNDSGQFML DFNDSRYLPF EGISVNDSGS LTLSFPDATD RQKALLESLS DIILHIRYTI R

UniProtKB: XptA2 protein

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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

Concentration1.5 mg/mL
BufferpH: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeJEOL 3200FSC
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 10.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 0.5 µm

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Image processing

Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.3 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 62247
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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