1P4D: F factor TraI Relaxase Domain

F factor TraI Relaxase Domain. Determined by X-ray diffraction at 2.6 Å resolution. Released 14 Oct 2003.

Method: X-ray diffraction
Resolution: 2.6 Å
Organism: Escherichia coli
Chains: 3
Atoms: 6,656
Mol. weight: 109.78 kDa
Ligands: MG
Released: 14 Oct 2003

Explore 1P4D in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

1P4D contains 36 α-helices and 46 β-strands across 3 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 13 helices, 15 β-strands

Element	Residues	Length	Sheet
β-strand	2-6	5	1
α-helix	7-8	2
α-helix	10-18	9
α-helix	20-22	3
β-strand	32-34	3	1
α-helix	36-40	5
α-helix	47-48	2
α-helix	49-57	9
β-strand	59	1	2
β-strand	65	1	2
β-strand	69-70	2	3
β-strand	73-74	2	3
β-strand	79-85	7	1
α-helix	88-95	8
α-helix	101-118	18
β-strand	122-127	6	4
β-strand	130-135	6	4
β-strand	141-148	8	1
β-strand	154-163	10	1
β-strand	166-168	3	5
β-strand	171-173	3	5
α-helix	185-191	7
α-helix	193-210	18
β-strand	216-217	2	6
β-strand	224-225	2	6
α-helix	231-234	4
α-helix	270-282	13
α-helix	288-303	16

Chain B: 11 helices, 15 β-strands

Element	Residues	Length	Sheet
β-strand	2-6	5	7
α-helix	10-18	9
α-helix	20-23	4
β-strand	32-34	3	7
α-helix	36-40	5
α-helix	49-57	9
β-strand	59	1	8
β-strand	65	1	8
β-strand	69	1	9
β-strand	74	1	9
β-strand	79-85	7	7
α-helix	88-95	8
α-helix	101-118	18
β-strand	122-127	6	10
β-strand	130-135	6	10
β-strand	141-148	8	7
β-strand	154-163	10	7
β-strand	166-168	3	11
β-strand	171-173	3	11
α-helix	185-190	6
α-helix	193-210	18
β-strand	216-217	2	12
β-strand	224-225	2	12
α-helix	231-234	4
α-helix	270-283	14
α-helix	288-302	15

Chain C: 12 helices, 16 β-strands

Element	Residues	Length	Sheet
β-strand	2-3	2	13
β-strand	6	1	13
α-helix	7-8	2
α-helix	12-14	3
α-helix	15-18	4
β-strand	32-34	3	13
α-helix	35-40	6
α-helix	53-56	4
β-strand	59-60	2	14
β-strand	64-65	2	14
β-strand	69	1	15
β-strand	74	1	15
β-strand	79-85	7	13
α-helix	88-94	7
α-helix	101-117	17
β-strand	122-126	5	16
β-strand	131-135	5	16
β-strand	141-148	8	13
β-strand	154-163	10	13
β-strand	168	1	17
β-strand	171	1	17
α-helix	185-191	7
α-helix	193-210	18
β-strand	216-217	2	18
α-helix	220-222	3
β-strand	224-225	2	18
α-helix	270-283	14
α-helix	288-303	16

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
TraI protein	A, B, C	protein	330	Escherichia coli	P14565 (AlphaFold model)

Sequence of entity 1 (A, B, C), FASTA

>1P4D_1 TraI protein (chains A, B, C)
MMSIAQVRSAGSAGNYYTDKDNYYVLGSMGERWAGRGAEQLGLQGSVDKDVFTRLLEGRL
PDGADLSRMQDGSNRHRPGYDLTFSAPKSVSMMAMLGGDKRLIDAHNQAVDFAVRQVEAL
ASTRVMTDGQSETVLTGNLVMALFNHDTSRDQEPQLHTHAVVANVTQHNGEWKTLSSDKV
GKTGFIENVYANQIAFGRLYREKLKEQVEALGYETEVVGKHGMWEMPGVPVEAFSGRSQT
IREAVGEDASLKSRDVAALDTRKSKQHVDPEIKMAEWMQTLKETGFDIRAYRDAADQRAD
LRTLTPGPASQDGPDVQQAVTQAIAGLSER

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	3

Water and common crystallization additives (EDO) are not listed.

Primary citation

Structural insights into single-stranded DNA binding and cleavage by F factor TraI. Datta, S., Larkin, C., Schildbach, J.F. Structure (2003) 11:1369-1379. DOI 10.1016/j.str.2003.10.001 · PubMed

Other PDB entries of the same protein (UniProt P14565 (AlphaFold model), which also has an AlphaFold model), best resolution first:

3FLD 2.4 Å, Crystal structure of the trai c-terminal domain
2Q7T 2.42 Å, Crystal Structure of the F plasmid TraI Relaxase Domain with the Scissile Thymidine Base
2A0I 2.72 Å, F Factor TraI Relaxase Domain bound to F oriT Single-stranded DNA
9F10 2.94 Å, CryoEM structure of the F plasmid relaxosome with TraI in its TE mode, without accessory…
2Q7U 3.0 Å, Crystal Structure of the F plasmid TraI Relaxase Domain with the Scissile Thymidine Base…
9F0Z 3.42 Å, CryoEM structure of the F plasmid relaxosome with truncated TraI1-863 in its TE mode,…
9F12 3.42 Å, CryoEM structure of the F plasmid relaxosome with oriT DNA ss-27_-3ds-2_+143 and TraI…
9F0Y 3.45 Å, CryoEM structure of the F plasmid relaxosome with TraI in its TE mode, derived from the…
9F11 3.68 Å, CryoEM structure of the F plasmid relaxosome with oriT DNA ss-27_+3ds+4_+143 and TraI…
9F0X 3.78 Å, CryoEM structure of the F plasmid relaxosome in its pre-initiation state, derived from…
2L8B TraI (381-569)

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