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FASTA Sequence PDB Format mmCIF Format
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9IXM

Cryo-em structure of lactobacillus casei ddmde bound with dna

PDB DOI: 10.2210/pdb9ixm/pdb

Classification: DNA BINDING PROTEIN/DNA
Organism(s): Anopheles Culicifacies , Rhodobacter Sphaeroides (Strain Atcc 17023 / Dsm 158 / Jcm 6121 / Nbrc 12203 / Ncimb 8253 / Ath 2.4.1.)

Deposited: 2024-07-29
Deposition Author(s): Chen, M.R. , Huang, P.P. , Xiao, Y.B.

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.26 Å

9ixm
Literature

Cryo-em structure of lactobacillus casei ddmde bound with dna

Chen, M.R. , Huang, P.P. , Xiao, Y.B.

Primary Citation of Related Structures: 9IXM


Proteins
Molecule Chains Sequence Length Organism Sequence
DdmD A 1192 Anopheles Culicifacies , Rhodobacter Sphaeroides (Strain Atcc 17023 / Dsm 158 / Jcm 6121 / Nbrc 12203 / Ncimb 8253 / Ath 2.4.1.) MQVSDFSGMIKKLQSQSPEHALMLLNAPTGTGKSYTIIRALCRYAIKHENFRAFFVTDQKKNLKEQDFEVAWREESGAVHKAFSERVAVVRSLEDTVNKLINDWDRQQIPDLYRSSPIFKKSLENLGNAFKSFGMMKENEFDLKNAWTMLSRAEYQVRRAMITILADKAHVKLKNISEAGASAFKLDSISKGKIREFVSKQPKADSKWLNETYPTFDLEKKQIIILTTAKFIKSYTPFFEKRSKAFRYSPILKDALVVLDEFDSTKKQILESAIDEALKIQADLNSLFVDLSKGLNKVNEGQLPAKLGKSFTFRDAFKEILNDAEQLTAEFKLDFLYKMEEQGRDSGFVMRVPQTNWVSVGKPWNAYFDEELRQVVLGRQPRNDLNFQRMLPRISVFLKGATKFILNRAREYQVSENQKLSSLDDAMTIEDACFSIYAALGLSKSQAKILFSLGHDFSSPTKVKTTYHAHSGRRFQQRGLSLFQFTNDPQHDLQTKINACFFNETPERYLLNLLSKANVLGLSATATLPTVLDNYDLGYLREMLGPRLLDGVHYLSDTTIKEFDFESRYAKQKIEVKVETGIVDRFFSEILPKNNQKIDNKKIWELDAELAKLVNCIPASEQSRIDKKYFARRYLNLFNSFVIFLTDPSMTSFLGLQSLLPGADGRMDENYIKETFTTLKDLVGGQDGVNTELRIVSSRNQEGIQEQLSEALNLVSQGGKRVYILSAYQTIGIGQNLQHEMNEFEREQAANIAPKGVSKSDRRQHTIDLAGMYLGEVTHILSSNLPFRMDAAGLRSIIEQEYLFDANEINIKYLNKYLKGLQHQRLERHPEYARSLYVSYSRTIIQALGRMNRSFNKMPLIRLVMPVNVLQMVTDSGIDVEKTSQEYRCLLTAAKDWERDFEKPSAEIAKQNATFNTFRDYRFVLAYLQTSKSWAQIYHDTRWFYVRHPTVSDKDLKSSQVFQQRDDEFGLQYLLNEHLDVSYEVKPINHDNGQFDFSGTGMEVSAEAAGLVAMCRYPGLKEAFESLDIPTKWEPNERILNPAQFYNYRGLLGEVSGQFIFQNEWSLKLADFGKPENYELFDFHWEGKVVIDFKNWRDAPDVDTKAERQKVEAKLAKLQANTQREWRVIIINILASNQTRPVMTVDGKILEISGLIDHQGKFLLTPEQKLNVWRFLNGTAVNDSNDTIRLQN
DdmD C 1192 Anopheles Culicifacies , Rhodobacter Sphaeroides (Strain Atcc 17023 / Dsm 158 / Jcm 6121 / Nbrc 12203 / Ncimb 8253 / Ath 2.4.1.) MQVSDFSGMIKKLQSQSPEHALMLLNAPTGTGKSYTIIRALCRYAIKHENFRAFFVTDQKKNLKEQDFEVAWREESGAVHKAFSERVAVVRSLEDTVNKLINDWDRQQIPDLYRSSPIFKKSLENLGNAFKSFGMMKENEFDLKNAWTMLSRAEYQVRRAMITILADKAHVKLKNISEAGASAFKLDSISKGKIREFVSKQPKADSKWLNETYPTFDLEKKQIIILTTAKFIKSYTPFFEKRSKAFRYSPILKDALVVLDEFDSTKKQILESAIDEALKIQADLNSLFVDLSKGLNKVNEGQLPAKLGKSFTFRDAFKEILNDAEQLTAEFKLDFLYKMEEQGRDSGFVMRVPQTNWVSVGKPWNAYFDEELRQVVLGRQPRNDLNFQRMLPRISVFLKGATKFILNRAREYQVSENQKLSSLDDAMTIEDACFSIYAALGLSKSQAKILFSLGHDFSSPTKVKTTYHAHSGRRFQQRGLSLFQFTNDPQHDLQTKINACFFNETPERYLLNLLSKANVLGLSATATLPTVLDNYDLGYLREMLGPRLLDGVHYLSDTTIKEFDFESRYAKQKIEVKVETGIVDRFFSEILPKNNQKIDNKKIWELDAELAKLVNCIPASEQSRIDKKYFARRYLNLFNSFVIFLTDPSMTSFLGLQSLLPGADGRMDENYIKETFTTLKDLVGGQDGVNTELRIVSSRNQEGIQEQLSEALNLVSQGGKRVYILSAYQTIGIGQNLQHEMNEFEREQAANIAPKGVSKSDRRQHTIDLAGMYLGEVTHILSSNLPFRMDAAGLRSIIEQEYLFDANEINIKYLNKYLKGLQHQRLERHPEYARSLYVSYSRTIIQALGRMNRSFNKMPLIRLVMPVNVLQMVTDSGIDVEKTSQEYRCLLTAAKDWERDFEKPSAEIAKQNATFNTFRDYRFVLAYLQTSKSWAQIYHDTRWFYVRHPTVSDKDLKSSQVFQQRDDEFGLQYLLNEHLDVSYEVKPINHDNGQFDFSGTGMEVSAEAAGLVAMCRYPGLKEAFESLDIPTKWEPNERILNPAQFYNYRGLLGEVSGQFIFQNEWSLKLADFGKPENYELFDFHWEGKVVIDFKNWRDAPDVDTKAERQKVEAKLAKLQANTQREWRVIIINILASNQTRPVMTVDGKILEISGLIDHQGKFLLTPEQKLNVWRFLNGTAVNDSNDTIRLQN
DdmE B 715 Anopheles Culicifacies , Rhodobacter Sphaeroides (Strain Atcc 17023 / Dsm 158 / Jcm 6121 / Nbrc 12203 / Ncimb 8253 / Ath 2.4.1.) MEQQSMIRTTRLDYKINMMQLQADFKFLVVKIIDRSAFKDYNKLLASWSPEAVTSIRGRYKKGDYLMMFRQLPAIPTIAGLELHEILLEDMGEFKIYPNHLLQLLLNQQSANEKSLLEPCKTPELLISGEEWYREFRDMRQQYYALKLKVNWQQDLEMSVQTFTQVTEFQWDKQIYQFDEKRGRFQLCYQPSPGIYFVQGNHSANRNYIDFLSLQNKSSFYKSKVGVVQLVLDNLNLNAEKYLLRPVTFHKSLVEHSSRLKLSKRETIWQQLAGSSLNIYAQVNDRLSQELADQLADHLIRSQLVRKNSVHVVRSQKIQSGFNIQVIRDVRGRAAEDGYEVAKNDQIVQHLTVENFGHYQEGDKEITWKPKVSGKHHDPARDVAIVKLIQELCIKRDLANGKLKTVEPKLASLTQPLEFYYFAFLKKSFDPEVMVIKLAFTPEMELRFSKKKVRLNALTSDDEYTQVCKRVFDSLAAPKFYSAWDSVDCVVRSGNKQLLIQRLNRTIMPDGKQIRKQLELNRPDKTLWRDKVVEELGELRPMVSGDSDYVAAYEQLQALVTGMRPSFPLKDLDEAARKAGLNPKRRDMRQVNQFLTENATFTLKTTLQRELPDSPLAGMKWIGLTRIEEGEGHFNTFYFVGSDKSLKPVVNRAVTLRRLLPLAGDAGIIDELFPKLAAMMSVEFVRSGQYTVVPYPVKYLREYWYSILRQHPEYR

Nucleic Acids / Hybrid
Molecule Chains Sequence Length Organism Sequence
DNA (30-MER) e 30 NA CACTAATAGATTAGAGCCGTCACGTATCAA
DNA (5'-D(P*TP*GP*AP*CP*GP*GP*CP*TP*CP*TP*AP*AP*TP*CP*T)-3') d 15 NA TGACGGCTCTAATCT
DNA (30-MER) f 30 NA TTGATACGACTGCCGAGATTAGATAAAGTG
Experimental Data

Method: ELECTRON MICROSCOPY

Deposited Date: 2024-07-29
Deposition Author(s): Chen, M.R. , Huang, P.P. , Xiao, Y.B.