3EJD: P450BioI

Crystal Structure of P450BioI in complex with hexadec-9Z-enoic acid ligated Acyl Carrier Protein. Determined by X-ray diffraction at 2.1 Å resolution. Released 7 Oct 2008.

Method: X-ray diffraction
Resolution: 2.1 Å
Organisms: Escherichia coli, Bacillus subtilis
Chains: 8
Atoms: 16,057
Mol. weight: 233.97 kDa
Ligands: ZMQ, HTG, HEM
Released: 7 Oct 2008

Explore 3EJD in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3EJD contains 112 α-helices and 64 β-strands across 8 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.

Chains A and E: 5 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	20-22	3
α-helix	23-35	13
β-strand	47	1	1
α-helix	58-69	12
α-helix	76-81	6
β-strand	84	1	1
α-helix	85-94	10

Chains B and F: 23 helices, 14 β-strands

Element	Residues	Length	Sheet
α-helix	10-13	4
α-helix	15-25	11
β-strand	28-33	6	2
β-strand	36-41	6	2
α-helix	44-52	9
β-strand	56-57	2	2
α-helix	70-77	8
α-helix	80-82	3
α-helix	87-95	9
α-helix	96-99	4
α-helix	101-105	5
α-helix	108-120	13
α-helix	123-125	3
β-strand	127-129	3	3
α-helix	130-135	6
α-helix	136-147	12
α-helix	151-153	3
α-helix	154-165	12
α-helix	166-168	3
α-helix	174-200	27
α-helix	206-212	7
α-helix	221-252	32
α-helix	254-262	9
α-helix	264-266	3
α-helix	267-277	11
β-strand	281	1	4
β-strand	283-288	6	2
β-strand	292-294	3	5
β-strand	297-299	3	5
β-strand	304-308	5	2
α-helix	309-312	4
α-helix	347-364	18
β-strand	369-370	2	3
β-strand	377	1	6
β-strand	383	1	4
β-strand	386	1	6
β-strand	390-392	3	3

Chains C and G: 5 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	20-22	3
α-helix	23-35	13
β-strand	47	1	7
α-helix	58-69	12
α-helix	76-81	6
β-strand	84	1	7
α-helix	85-92	8

Chain D: 24 helices, 14 β-strands

Element	Residues	Length	Sheet
α-helix	7-13	7
α-helix	15-25	11
β-strand	28-33	6	8
β-strand	36-41	6	8
α-helix	44-52	9
β-strand	56-57	2	8
α-helix	70-77	8
α-helix	80-82	3
α-helix	87-95	9
α-helix	96-99	4
α-helix	101-105	5
α-helix	108-120	13
α-helix	123-125	3
β-strand	127-129	3	9
α-helix	130-135	6
α-helix	136-147	12
α-helix	151-153	3
α-helix	154-166	13
α-helix	174-200	27
α-helix	206-212	7
α-helix	221-251	31
α-helix	254-262	9
α-helix	264-266	3
α-helix	267-277	11
β-strand	281	1	10
β-strand	283-288	6	8
β-strand	292-294	3	11
β-strand	297-299	3	11
α-helix	300	1
β-strand	304-308	5	8
α-helix	309-312	4
α-helix	340-342	3
α-helix	347-364	18
β-strand	369-370	2	9
β-strand	377	1	12
β-strand	383	1	10
β-strand	386	1	12
β-strand	390-392	3	9

Chain H: 22 helices, 14 β-strands

Element	Residues	Length	Sheet
α-helix	10-13	4
α-helix	15-25	11
β-strand	28-33	6	20
β-strand	36-41	6	20
α-helix	44-52	9
β-strand	56-57	2	20
α-helix	70-77	8
α-helix	80-82	3
α-helix	87-95	9
α-helix	96-99	4
α-helix	101-105	5
α-helix	108-120	13
β-strand	127-129	3	21
α-helix	130-135	6
α-helix	136-147	12
α-helix	151-153	3
α-helix	154-166	13
α-helix	174-200	27
α-helix	206-212	7
α-helix	221-251	31
α-helix	254-262	9
α-helix	264-266	3
α-helix	267-277	11
β-strand	281	1	22
β-strand	283-288	6	20
β-strand	292-294	3	23
β-strand	297-299	3	23
β-strand	304-308	5	20
α-helix	309-312	4
α-helix	340-342	3
α-helix	347-364	18
β-strand	369-370	2	21
β-strand	377	1	24
β-strand	383	1	22
β-strand	386	1	24
β-strand	390-392	3	21

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Acyl carrier protein	A, C, E, G	protein	97	Escherichia coli	P0A6A8 (AlphaFold model)
Biotin biosynthesis cytochrome P450-like enzyme	B, D, F, H	protein	404	Bacillus subtilis	P53554 (AlphaFold model)

Sequence of entity 1 (A, C, E, G), FASTA

>3EJD_1 Acyl carrier protein (chains A, C, E, G)
GSSHHHHHHSSGLVPRGSHMSTIEERVKKIIGEQLGVKQEEVTNNASFVEDLGADSLDTV
ELVMALEEEFDTEIPDEEAEKITTVQAAIDYINGHQA

Sequence of entity 2 (B, D, F, H), FASTA

>3EJD_2 Biotin biosynthesis cytochrome P450-like enzyme (chains B, D, F, H)
TIASSTASSEFLKNPYSFYDTLRAVHPIYKGSFLKYPGWYVTGYEETAAILKDARFKVRT
PLPESSTKYQDLSHVQNQMMLFQNQPDHRRLRTLASGAFTPRTTESYQPYIIETVHHLLD
QVQGKKKMEVISDFAFPLASFVIANIIGVPEEDREQLKEWAASLIQTIDFTRSRKALTEG
NIMAVQAMAYFKELIQKRKRHPQQDMISMLLKGREKDKLTEEEAASTCILLAIAGHETTV
NLISNSVLCLLQHPEQLLKLRENPDLIGTAVEECLRYESPTQMTARVASEDIDICGVTIR
QGEQVYLLLGAANRDPSIFTNPDVFDITRSPNPHLSFGHGHHVCLGSSLARLEAQIAINT
LLQRMPSLNLADFEWRYRPLFGFRALEELPVTFEASWSHPQFEK

Ligands and cofactors

ID	Name	Formula	Copies
ZMQ	S-[2-({N-[(2S)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alanyl}ami…	C27 H51 N2 O8 P S	4
HTG	heptyl 1-thio-beta-D-glucopyranoside	C13 H26 O5 S	8
HEM	Protoporphyrin IX containing FE	C34 H32 Fe N4 O4	4

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

Primary citation

Structural insights from a P450 Carrier Protein complex reveal how specificity is achieved in the P450(BioI) ACP complex. Cryle, M.J., Schlichting, I. Proc Natl Acad Sci U S A (2008) 105:15696-15701. DOI 10.1073/pnas.0805983105 · PubMed

Other PDB entries of the same protein (UniProt P0A6A8 (AlphaFold model), which also has an AlphaFold model), best resolution first:

1T8K 1.1 Å, Crystal Structure of apo acyl carrier protein from E. coli
1L0I 1.2 Å, Crystal structure of butyryl-ACP I62M mutant
9KA6 1.47 Å, Crystal structure of beta-ketoacyl-ACP synthase FabH C112Q in complex with acyl-ACP from…
2FAE 1.55 Å, Crystal structure of E. coli decanoyl-ACP
6OKC 1.55 Å, Crosslinked Crystal Structure of Type II Fatty Acid Synthase Ketosynthase, FabB, and…
6UXE 1.57 Å, Structure of the human mitochondrial desulfurase complex Nfs1-ISCU2(M140I)-ISD11 with…
2FAD 1.6 Å, Crystal structure of E. coli heptanoyl-ACP
7SQI 1.7 Å, Crosslinked Crystal Structure of Type II Fatty Acid Synthase Ketosynthase, FabB, and…
2FAC 1.76 Å, Crystal structure of E. coli hexanoyl-ACP
6W1D 1.79 Å, Structure of human mitochondrial complex Nfs1-ISCU2 (WT)-ISD11 with E.coli ACP1 at 1.8 A…
6U0J 1.9 Å, Crosslinked Crystal Structure of Malonyl-CoA Acyl Carrier Protein Transacylase, FabD,…
6WIH 1.9 Å, N-terminal mutation of ISCU2 (L35H36) traps Nfs1 Cys loop in the active site of ISCU2…

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