E.coli gyrase holocomplex with 217 bp DNA and Albi-1 (site TG)
Resolution: 3.25 Å
EM Method: Single-particle
Fitted PDBs: 7z9k
Q-score: 0.449
Michalczyk E, Hommernick K, Behroz I, Kulike M, Pakosz-Stepien Z, Mazurek L, Seidel M, Kunert M, Santos K, von Moeller H, Loll B, Weston JB, Mainz A, Heddle JG, Sussmuth RD, Ghilarov D
Nat Catal (2023) 6 pp. 52-67 [ DOI: doi:10.1038/s41929-022-00904-1 Pubmed: 36741192 ]
- Dna gyrase subunit b (90 kDa, Protein from Escherichia coli str. K-12 substr. MG1655)
- Dna (5'-d(p*ap*gp*ap*ap*tp*cp*ap*gp*gp*cp*ap*tp*ap*a)-3') (4 kDa, DNA from Escherichia phage Mu)
- Dna (5'-d(*gp*ap*tp*tp*tp*tp*ap*tp*gp*cp*cp*tp*gp*ap*tp*tp*cp*t)-3') (5 kDa, DNA from Escherichia phage Mu)
- Dna (5'-d(p*ap*ap*ap*tp*cp*tp*gp*tp*gp*cp*gp*gp*gp*t)-3') (4 kDa, DNA from Escherichia phage Mu)
- Dna (5'-d(*ap*ap*tp*cp*ap*cp*cp*cp*gp*cp*ap*cp*ap*gp*ap*tp*tp*t)-3') (5 kDa, DNA from Escherichia phage Mu)
- Escherichia coli gyrase holocomplex with 217 bp phage mu sgs dna and albicidin stabilised by adpnp (Complex)
- Dna gyrase subunit a (97 kDa, Protein from Escherichia coli str. K-12 substr. MG1655)
- Escherichia coli gyrase holocomplex (Complex from Escherichia coli str. K-12 substr. MG1655)
- Magnesium ion (24 Da, Ligand)
- 217 bp phage mu sgs dna (Complex from Escherichia phage Mu)
- 4-[[4-[[5-[[(2s)-2-[[5-[(4-cyanophenyl)carbonylamino]pyridin-2-yl]carbonylamino]-3-(1h-1,2,3-triazol-4-yl)propanoyl]amino]pyridin-2-yl]carbonylamino]-2-oxidanyl-3-propan-2-yloxy-phenyl]carbonylamino]benzoic acid (837 Da, Ligand)
E.coli gyrase holocomplex with 217 bp DNA and albicidin
Resolution: 3.06 Å
EM Method: Single-particle
Fitted PDBs: 7z9c
Q-score: 0.517
Michalczyk E, Hommernick K, Behroz I, Kulike M, Pakosz-Stepien Z, Mazurek L, Seidel M, Kunert M, Santos K, von Moeller H, Loll B, Weston JB, Mainz A, Heddle JG, Sussmuth RD, Ghilarov D
Nat Catal (2023) 6 pp. 52-67 [ DOI: doi:10.1038/s41929-022-00904-1 Pubmed: 36741192 ]
- Albicidin (842 Da, Ligand)
- Dna gyrase subunit b (90 kDa, Protein from Escherichia coli str. K-12 substr. MG1655)
- Dna (5'-d(p*ap*gp*ap*ap*tp*cp*ap*gp*gp*cp*ap*tp*ap*a)-3') (4 kDa, DNA from Escherichia phage Mu)
- Dna (5'-d(*gp*ap*tp*tp*tp*tp*ap*tp*gp*cp*cp*tp*gp*ap*tp*tp*cp*t)-3') (5 kDa, DNA from Escherichia phage Mu)
- Dna (5'-d(p*ap*ap*ap*tp*cp*tp*gp*tp*gp*cp*gp*gp*gp*t)-3') (4 kDa, DNA from Escherichia phage Mu)
- Dna (5'-d(*ap*ap*tp*cp*ap*cp*cp*cp*gp*cp*ap*cp*ap*gp*ap*tp*tp*t)-3') (5 kDa, DNA from Escherichia phage Mu)
- Escherichia coli gyrase holocomplex with 217 bp phage mu sgs dna and albicidin stabilised by adpnp (Complex)
- Water (18 Da, Ligand)
- Dna gyrase subunit a (97 kDa, Protein from Escherichia coli str. K-12 substr. MG1655)
- Escherichia coli gyrase holocomplex (Complex from Escherichia coli str. K-12 substr. MG1655)
- Magnesium ion (24 Da, Ligand)
- 217 bp phage mu sgs dna (Complex from Escherichia phage Mu)
E.coli gyrase holocomplex with 217 bp DNA and Albi-2
Resolution: 3.25 Å
EM Method: Single-particle
Fitted PDBs: 7z9g
Q-score: 0.466
Michalczyk E, Hommernick K, Behroz I, Kulike M, Pakosz-Stepien Z, Mazurek L, Seidel M, Kunert M, Santos K, von Moeller H, Loll B, Weston JB, Mainz A, Heddle JG, Sussmuth RD, Ghilarov D
Nat Catal (2023) 6 pp. 52-67 [ DOI: doi:10.1038/s41929-022-00904-1 Pubmed: 36741192 ]
- Dna gyrase subunit b (90 kDa, Protein from Escherichia coli str. K-12 substr. MG1655)
- Dna (5'-d(p*ap*gp*ap*ap*tp*cp*ap*gp*gp*cp*ap*tp*ap*a)-3') (4 kDa, DNA from Escherichia phage Mu)
- Dna (5'-d(*gp*ap*tp*tp*tp*tp*ap*tp*gp*cp*cp*tp*gp*ap*tp*tp*cp*t)-3') (5 kDa, DNA from Escherichia phage Mu)
- Dna (5'-d(p*ap*ap*ap*tp*cp*tp*gp*tp*gp*cp*gp*gp*gp*t)-3') (4 kDa, DNA from Escherichia phage Mu)
- Dna (5'-d(*ap*ap*tp*cp*ap*cp*cp*cp*gp*cp*ap*cp*ap*gp*ap*tp*tp*t)-3') (5 kDa, DNA from Escherichia phage Mu)
- Escherichia coli gyrase holocomplex with 217 bp phage mu sgs dna and albicidin stabilised by adpnp (Complex)
- Water (18 Da, Ligand)
- Dna gyrase subunit a (97 kDa, Protein from Escherichia coli str. K-12 substr. MG1655)
- 4-[[3-(2-azanylethoxy)-2-oxidanyl-4-[[5-[[(2~{s})-2-[[4-[(6-oxidanylnaphthalen-2-yl)carbonylamino]phenyl]carbonylamino]-3-(1~{h}-1,2,3-triazol-4-yl)propanoyl]amino]pyridin-2-yl]carbonylamino]phenyl]carbonylamino]-3-methoxy-2-oxidanyl-benzoic acid (924 Da, Ligand)
- Escherichia coli gyrase holocomplex (Complex from Escherichia coli str. K-12 substr. MG1655)
- Magnesium ion (24 Da, Ligand)
- 217 bp phage mu sgs dna (Complex from Escherichia phage Mu)
E.coli gyrase holocomplex with 217 bp DNA and Albi-1 (site AA)
Resolution: 3.3 Å
EM Method: Single-particle
Fitted PDBs: 7z9m
Q-score: 0.444
Michalczyk E, Hommernick K, Behroz I, Kulike M, Pakosz-Stepien Z, Mazurek L, Seidel M, Kunert M, Santos K, von Moeller H, Loll B, Weston JB, Mainz A, Heddle JG, Sussmuth RD, Ghilarov D
Nat Catal (2023) 6 pp. 52-67 [ DOI: doi:10.1038/s41929-022-00904-1 Pubmed: 36741192 ]
- Dna gyrase subunit b (90 kDa, Protein from Escherichia coli str. K-12 substr. MG1655)
- Dna (5'-d(p*ap*gp*ap*ap*tp*cp*ap*gp*gp*cp*ap*tp*ap*a)-3') (4 kDa, DNA from Escherichia phage Mu)
- Dna (5'-d(*gp*ap*tp*tp*tp*tp*ap*tp*gp*cp*cp*tp*gp*ap*tp*tp*cp*t)-3') (5 kDa, DNA from Escherichia phage Mu)
- Dna (5'-d(p*ap*ap*ap*tp*cp*tp*gp*tp*gp*cp*gp*gp*gp*t)-3') (4 kDa, DNA from Escherichia phage Mu)
- Dna (5'-d(*ap*ap*tp*cp*ap*cp*cp*cp*gp*cp*ap*cp*ap*gp*ap*tp*tp*t)-3') (5 kDa, DNA from Escherichia phage Mu)
- Escherichia coli gyrase holocomplex with 217 bp phage mu sgs dna and albicidin stabilised by adpnp (Complex)
- Water (18 Da, Ligand)
- Dna gyrase subunit a (97 kDa, Protein from Escherichia coli str. K-12 substr. MG1655)
- Escherichia coli gyrase holocomplex (Complex from Escherichia coli str. K-12 substr. MG1655)
- Magnesium ion (24 Da, Ligand)
- 217 bp phage mu sgs dna (Complex from Escherichia phage Mu)
- 4-[[4-[[5-[[(2s)-2-[[5-[(4-cyanophenyl)carbonylamino]pyridin-2-yl]carbonylamino]-3-(1h-1,2,3-triazol-4-yl)propanoyl]amino]pyridin-2-yl]carbonylamino]-2-oxidanyl-3-propan-2-yloxy-phenyl]carbonylamino]benzoic acid (837 Da, Ligand)