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- EMDB-17088: EcoR124I bound to dsDNA -

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Basic information

Entry
Database: EMDB / ID: EMD-17088
TitleEcoR124I bound to dsDNA
Map dataType IC restriction modification system EcoR124I bound to 38-mer dsDNA
Sample
  • Complex: EcoR124I+DNA
    • Other: Type I C restriction-modification complex EcoR124I
KeywordsPentameric complex / restriction-modification enzyme / restriction endonuclease / methyltransferase / ANTIVIRAL PROTEIN
Biological speciesEscherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.7 Å
AuthorsPradeep HN
Funding support Czech Republic, 1 items
OrganizationGrant numberCountry
Not funded Czech Republic
CitationJournal: To Be Published
Title: EcoR124I bound to dsDNA
Authors: Pradeep HN
History
DepositionApr 10, 2023-
Header (metadata) releaseJun 7, 2023-
Map releaseJun 7, 2023-
UpdateJun 7, 2023-
Current statusJun 7, 2023Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_17088.png

Downloads & links

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Map

FileDownload / File: emd_17088.map.gz / Format: CCP4 / Size: 98.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationType IC restriction modification system EcoR124I bound to 38-mer dsDNA
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.71 Å/pix.
x 296 pix.
= 211.344 Å		0.71 Å/pix.
x 296 pix.
= 211.344 Å		0.71 Å/pix.
x 296 pix.
= 211.344 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.714 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.744
Minimum - Maximum-0.825075 - 2.0479963
Average (Standard dev.)0.012050212 (±0.07978109)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions296296296
Spacing296296296
CellA=B=C: 211.344 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Type IC restriction modification system EcoR124I bound to...

Fileemd_17088_half_map_1.map
AnnotationType IC restriction modification system EcoR124I bound to 38-mer dsDNA - halfmap A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Type IC restriction modification system EcoR124I bound to...

Fileemd_17088_half_map_2.map
AnnotationType IC restriction modification system EcoR124I bound to 38-mer dsDNA - halfmap B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : EcoR124I+DNA

EntireName: EcoR124I+DNA
Components
  • Complex: EcoR124I+DNA
    • Other: Type I C restriction-modification complex EcoR124I

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Supramolecule #1: EcoR124I+DNA

SupramoleculeName: EcoR124I+DNA / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 0.4 kDa/nm

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Macromolecule #1: Type I C restriction-modification complex EcoR124I

MacromoleculeName: Type I C restriction-modification complex EcoR124I / type: other / ID: 1
Details: Subunit HsdR (2x); Subunit HsdM (2x); Subunit HsdS (1x)
Classification: other
Source (natural)Organism: Escherichia coli (E. coli)
SequenceString: MTHQTHTIAE SNNFIVLDKY IKAEPTGDSY QSESDLEREL IQDLRNQGYE FISVKSQSAM LANVREQLQ NLNGVVFNDS EWRRFTEQYL DNPSDGILDK TRKIHIDYIC DFIFDDERLE N IYLIDKKN LMRNKVQIIQ QFEQAGSHAN RYDVTILVNG LPLVQIELKK ...String:
MTHQTHTIAE SNNFIVLDKY IKAEPTGDSY QSESDLEREL IQDLRNQGYE FISVKSQSAM LANVREQLQ NLNGVVFNDS EWRRFTEQYL DNPSDGILDK TRKIHIDYIC DFIFDDERLE N IYLIDKKN LMRNKVQIIQ QFEQAGSHAN RYDVTILVNG LPLVQIELKK RGVAIREAFN QI HRYSKES FNSENSLFKY LQLFVISNGT DTRYFANTTK RDKNSFDFTM NWAKSDNTLI KDL KDFTAT CFQKHTLLNV LVNYSVFDSS QTLLVMRPYQ IAATERILWK IKSSFTAKNW SKPE SGGYI WHTTGSGKTL TSFKAARLAT ELDFIDKVFF VVDRKDLDYQ TMKEYQRFSP DSVNG SENT AGLKRNLDKD DNKIIVTTIQ KLNNLMKAES DLPVYNQQVV FIFDECHRSQ FGEAQK NLK KKFKRYYQFG FTGTPIFPEN ALGSETTASV FGRELHSYVI TDAIRDEKVL KFKVDYN DV RPQFKSLETE TDEKKLSAAE NQQAFLHPMR IQEITQYILN NFRQKTHRTF PGSKGFNA M LAVSSVDAAK AYYATFKRLQ EEAANKSATY KPLRIATIFS FAANEEQNAI GEISDETFD TSAMDSSAKE FLDAAIREYN SHFKTNFSTD SNGFQNYYRD LAQRVKNQDI DLLIVVGMFL TGFDAPTLN TLFVDKNLRY HGLMQAFSRT NRIYDATKTF GNIVTFRDLE RSTIDAITLF G DKNTKNVV LEKSYTEYME GFTDAATGEA KRGFMTVVSE LEQRFPDPTS IESEKEKKDF VK LFGEYLR AENILQNYDE FATLKALQQI DLSDPVAVEK FKAEHYVDDE KFAELQTIRL PAD RKIQDY RSAYNDIRDW QRREKEAEKK EKSTTDWDDV VFEVDLLKSQ EINLDYILGL IFEH NRQNK GKGEMIEEVK RLIRSSLGNR AKEGLVVDFI QQTNLDDLPD KASIIDAFFT FAQRE QQRE AEALIKEENL NEDAAKRYIR TSLKREYATE NGTELNETLP KLSPLNPQYK TKKQAV FRK SSRLLRSLKA MKMTSIQQRA ELHRQIWQIA NDVRGSVDGW DFKQYVLGAL FYRFISE NF SSYIEAGDDS ICYAKLDDSV ITDDIKDDAI KTKGYFIYPS QLFCNVAAKA NTNDRLNA D LNSIFVAIES SAYGYPSEAD IKGLFADFDT TSNRLGNTVK DKNARLAAVL KGVEGLKLG DFNEHQIDLF GDAYEFLISN YAANAGKSGG EFFTPQHVSK LIAQLAMHGQ THVNKIYDPA AGSGSLLLQ AKKQFDNHII EEGFFGQEIN HTTYNLARMN MFLHNINYDK FDIKLGNTLT E PHFRDEKP FDAIVSNPPY SVKWIGSDDP TLINDERFAP AGVLAPKSKA DFAFVLHALN YL SAKGRAA IVCFPGIFYR GGAEQKIRQY LVDNNYVETV ISLAPNLFFG TTIAVNILVL SKH KTDTNV QFIDASELFK KETNNNILTD AHIEQIMQVF ASKEDVAHLA KSVAFETVVA NDYN LSVSS YVEAKDNREI IDIAELNAEL KTTVSKIDQL RKDIDAIVAE IEGCEVQKMS EMSYL EKLL DGVEVEWLPL GEITKYEQPT KYLVKAKDYH DTYTIPVLTA GKTFILGYTN ETHGIY QAS KAPVIIFDDF TTANKWVDFD FKAKSSAMKM VTSCDDNKTL LKYVYYWLNT LPSEFAE GD HKRQWISNYS QKKIPIPCPD NPEKSLAIQS EIVRILDKFT ALTAELTAEL NMRKKQYN Y YRDQLLSFKE GEVEWKTLGE IGKWYGGGTP SKNKIEFWEN GSIPWISPKD MGRTLVDSS EDYITEEAVL HSSTKLIPAN SIAIVVRSSI LDKVLPSALI KVPATLNQDM KAVIPHENIL VKYIYHMIG SRGSDILRAA KKTGGSVASI DSKKLFSFKI PVPNINEQQR IVEILDKFDT L TNSITEGL PREIELRQKQ YEYYRDLLFS FPKPETVSNM KMTSIQQRAE LHRQIWQIAN DV RGSVDGW DFKQYVLGAL FYRFISENFS SYIEAGDDSI CYAKLDDSVI TDDIKDDAIK TKG YFIYPS QLFCNVAAKA NTNDRLNADL NSIFVAIESS AYGYPSEADI KGLFADFDTT SNRL GNTVK DKNARLAAVL KGVEGLKLGD FNEHQIDLFG DAYEFLISNY AANAGKSGGE FFTPQ HVSK LIAQLAMHGQ THVNKIYDPA AGSGSLLLQA KKQFDNHIIE EGFFGQEINH TTYNLA RMN MFLHNINYDK FDIKLGNTLT EPHFRDEKPF DAIVSNPPYS VKWIGSDDPT LINDERF AP AGVLAPKSKA DFAFVLHALN YLSAKGRAAI VCFPGIFYRG GAEQKIRQYL VDNNYVET V ISLAPNLFFG TTIAVNILVL SKHKTDTNVQ FIDASELFKK ETNNNILTDA HIEQIMQVF ASKEDVAHLA KSVAFETVVA NDYNLSVSSY VEAKDNREII DIAELNAELK TTVSKIDQLR KDIDAIVAE IEGCEVQKMT HQTHTIAESN NFIVLDKYIK AEPTGDSYQS ESDLERELIQ D LRNQGYEF ISVKSQSAML ANVREQLQNL NGVVFNDSEW RRFTEQYLDN PSDGILDKTR KI HIDYICD FIFDDERLEN IYLIDKKNLM RNKVQIIQQF EQAGSHANRY DVTILVNGLP LVQ IELKKR GVAIREAFNQ IHRYSKESFN SENSLFKYLQ LFVISNGTDT RYFANTTKRD KNSF DFTMN WAKSDNTLIK DLKDFTATCF QKHTLLNVLV NYSVFDSSQT LLVMRPYQIA ATERI LWKI KSSFTAKNWS KPESGGYIWH TTGSGKTLTS FKAARLATEL DFIDKVFFVV DRKDLD YQT MKEYQRFSPD SVNGSENTAG LKRNLDKDDN KIIVTTIQKL NNLMKAESDL PVYNQQV VF IFDECHRSQF GEAQKNLKKK FKRYYQFGFT GTPIFPENAL GSETTASVFG RELHSYVI T DAIRDEKVLK FKVDYNDVRP QFKSLETETD EKKLSAAENQ QAFLHPMRIQ EITQYILNN FRQKTHRTFP GSKGFNAMLA VSSVDAAKAY YATFKRLQEE AANKSATYKP LRIATIFSFA ANEEQNAIG EISDETFDTS AMDSSAKEFL DAAIREYNSH FKTNFSTDSN GFQNYYRDLA Q RVKNQDID LLIVVGMFLT GFDAPTLNTL FVDKNLRYHG LMQAFSRTNR IYDATKTFGN IV TFRDLER STIDAITLFG DKNTKNVVLE KSYTEYMEGF TDAATGEAKR GFMTVVSELE QRF PDPTSI ESEKEKKDFV KLFGEYLRAE NILQNYDEFA TLKALQQIDL SDPVAVEKFK AEHY VDDEK FAELQTIRLP ADRKIQDYRS AYNDIRDWQR REKEAEKKEK STTDWDDVVF EVDLL KSQE INLDYILGLI FEHNRQNKGK GEMIEEVKRL IRSSLGNRAK EGLVVDFIQQ TNLDDL PDK ASIIDAFFTF AQREQQREAE ALIKEENLNE DAAKRYIRTS LKREYATENG TELNETL PK LSPLNPQYKT KKQAVFRKSS RLLRSLKA
Recombinant expressionOrganism: Escherichia coli (E. coli)

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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

Concentration1.2 mg/mL
BufferpH: 7.5 / Details: 20 mM NaCl, 50 mM HEPEs
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: CONTINUOUS
VitrificationCryogen name: ETHANE / Chamber humidity: 95 %
DetailsThis sample is heterogeneous

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Electron microscopy

MicroscopeTFS GLACIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 200 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

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Image processing

Startup modelType of model: NONE
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 4.7 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 30000
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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