3eje

Crystal Structure of P450BioI in complex with octadec-9Z-enoic acid ligated Acyl Carrier Protein

Method: X-RAY DIFFRACTION

▼

1. Protein Identity and Related Structures Protein Identity & Related Structures

Acyl carrier protein

Escherichia coli

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	Biotin biosynthesis cytochrome P450-like enzyme × 1 （P53554） S-[2-({N-[(2S)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alanyl}amino)ethyl] (9Z)-octadec-9-enethioate × 1 heptyl 1-thio-beta-D-glucopyranoside × 2 PROTOPORPHYRIN IX CONTAINING FE × 1 water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	Biotin biosynthesis cytochrome P450-like enzyme × 1 （P53554） S-[2-({N-[(2S)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alanyl}amino)ethyl] (9Z)-octadec-9-enethioate × 1 heptyl 1-thio-beta-D-glucopyranoside × 2 PROTOPORPHYRIN IX CONTAINING FE × 1 water × 2	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 2	Biotin biosynthesis cytochrome P450-like enzyme × 1 （P53554） S-[2-({N-[(2S)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alanyl}amino)ethyl] (9Z)-octadec-9-enethioate × 1 heptyl 1-thio-beta-D-glucopyranoside × 1 PROTOPORPHYRIN IX CONTAINING FE × 1 water × 2	Consistent with protein count
4	Protein heterocomplex	Heteromer	Protein 2	Biotin biosynthesis cytochrome P450-like enzyme × 1 （P53554） S-[2-({N-[(2S)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alanyl}amino)ethyl] (9Z)-octadec-9-enethioate × 1 heptyl 1-thio-beta-D-glucopyranoside × 2 PROTOPORPHYRIN IX CONTAINING FE × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	ACP_ECOLI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 20–97； UniProt 1–78 Author chain C； PDBConstruct 20–97； UniProt 1–78 Author chain E； PDBConstruct 20–97； UniProt 1–78 Author chain G； PDBConstruct 20–97； UniProt 1–78

Biotin biosynthesis cytochrome P450-like enzyme

Bacillus subtilis

UniProt P53554

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	Acyl carrier protein × 1 （P0A6A8） S-[2-({N-[(2S)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alanyl}amino)ethyl] (9Z)-octadec-9-enethioate × 1 heptyl 1-thio-beta-D-glucopyranoside × 2 PROTOPORPHYRIN IX CONTAINING FE × 1 water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	Acyl carrier protein × 1 （P0A6A8） S-[2-({N-[(2S)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alanyl}amino)ethyl] (9Z)-octadec-9-enethioate × 1 heptyl 1-thio-beta-D-glucopyranoside × 2 PROTOPORPHYRIN IX CONTAINING FE × 1 water × 2	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 2	Acyl carrier protein × 1 （P0A6A8） S-[2-({N-[(2S)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alanyl}amino)ethyl] (9Z)-octadec-9-enethioate × 1 heptyl 1-thio-beta-D-glucopyranoside × 1 PROTOPORPHYRIN IX CONTAINING FE × 1 water × 2	Consistent with protein count
4	Protein heterocomplex	Heteromer	Protein 2	Acyl carrier protein × 1 （P0A6A8） S-[2-({N-[(2S)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alanyl}amino)ethyl] (9Z)-octadec-9-enethioate × 1 heptyl 1-thio-beta-D-glucopyranoside × 2 PROTOPORPHYRIN IX CONTAINING FE × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	BIOI_BACSU
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–394； UniProt 2–395 Author chain D； PDBConstruct 1–394； UniProt 2–395 Author chain F； PDBConstruct 1–394； UniProt 2–395 Author chain H； PDBConstruct 1–394； UniProt 2–395

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	3eje
Deposition date deposition_date	2008-09-18
Structure title title	Crystal Structure of P450BioI in complex with octadec-9Z-enoic acid ligated Acyl Carrier Protein
Keywords keywords	;Protein-Protein Complex, Cytochrome P450 Fold, Carrier Protein, 4-Helix Bundle, Fatty acid biosynthesis, Lipid synthesis, Phosphopantetheine, Biotin biosynthesis, Heme, Iron, Metal-binding, Monooxygenase, Oxidoreductase, OXIDOREDUCTASE-LIPID TRANSPORT COMPLEX ;; OXIDOREDUCTASE/LIPID TRANSPORT
Experimental Method method	X-RAY DIFFRACTION

▼

3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

3eje__assembly_2__model_1

Assembly 2 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

3eje__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3eje__assembly_2__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	24.76 Å
Rg (electron density)	23.57 Å
Total Rg	24.44 Å
Atom count	3787
Residues	463
Excluded volume	67636 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3eje__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`3eje__assembly_2__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`3eje__assembly_3__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`3eje__assembly_4__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download

▶

4. Crystallography and Experiment 4. Crystallography & Experiment

▶

5. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Description description	Acyl carrier protein
Molecular weight formula_weight	10685.6 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,C,E,G
Atom count atom_count	15827

GSSHHHHHHSSGLVPRGSHMSTIEERVKKIIGEQLGVKQEEVTNNASFVEDLGADSLDTVELVMALEEEFDTEIPDEEAEKITTVQAAIDYINGHQA

Source Source

Source organism organism	Escherichia coli
NCBI taxonomy ID ncbi_taxonomy_id	83333
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Biotin biosynthesis cytochrome P450-like enzyme
Molecular weight formula_weight	45988.4 kDa
EC 编号 ec_number	1.14.-.-
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,D,F,H

TIASSTASSEFLKNPYSFYDTLRAVHPIYKGSFLKYPGWYVTGYEETAAILKDARFKVRTPLPESSTKYQDLSHVQNQMMLFQNQPDHRRLRTLASGAFTPRTTESYQPYIIETVHHLLDQVQGKKKMEVISDFAFPLASFVIANIIGVPEEDREQLKEWAASLIQTIDFTRSRKALTEGNIMAVQAMAYFKELIQKRKRHPQQDMISMLLKGREKDKLTEEEAASTCILLAIAGHETTVNLISNSVLCLLQHPEQLLKLRENPDLIGTAVEECLRYESPTQMTARVASEDIDICGVTIRQGEQVYLLLGAANRDPSIFTNPDVFDITRSPNPHLSFGHGHHVCLGSSLARLEAQIAINTLLQRMPSLNLADFEWRYRPLFGFRALEELPVTFEASWSHPQFEK

Source Source

Source organism organism	Bacillus subtilis
NCBI taxonomy ID ncbi_taxonomy_id	1423
Host organism host_organism	Escherichia coli

Entity 3 Entity 3 non-polymer

Description description	S-[2-({N-[(2S)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alanyl}amino)ethyl] (9Z)-octadec-9-enethioate
Molecular weight formula_weight	622.8 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 4 Entity 4 non-polymer

Description description	heptyl 1-thio-beta-D-glucopyranoside
Molecular weight formula_weight	294.4 kDa
Source method src_method	syn
Copy count entity_count	7

Entity 5 Entity 5 non-polymer

Description description	PROTOPORPHYRIN IX CONTAINING FE
Molecular weight formula_weight	616.5 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	806

▼

6. Fold Classification (SCOP + CATH) 24 domains

SCOP 2.08 (12 domains)

Domain ID domain_id	d3ejea2
Class class	a — All alpha proteins
Fold Fold fold	a.28 — Acyl carrier protein-like
Superfamily Superfamily superfamily	a.28.1 — ACP-like
Family Family family	a.28.1.1 — Acyl-carrier protein (ACP)

Domain ID domain_id	d3ejea3
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d3ejeb_
Class class	a — All alpha proteins
Fold Fold fold	a.104 — Cytochrome P450
Superfamily Superfamily superfamily	a.104.1 — Cytochrome P450
Family Family family	a.104.1.0 — automated matches

Domain ID domain_id	d3ejec2
Class class	a — All alpha proteins
Fold Fold fold	a.28 — Acyl carrier protein-like
Superfamily Superfamily superfamily	a.28.1 — ACP-like
Family Family family	a.28.1.1 — Acyl-carrier protein (ACP)

Domain ID domain_id	d3ejec3
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d3ejed_
Class class	a — All alpha proteins
Fold Fold fold	a.104 — Cytochrome P450
Superfamily Superfamily superfamily	a.104.1 — Cytochrome P450
Family Family family	a.104.1.0 — automated matches

Domain ID domain_id	d3ejee2
Class class	a — All alpha proteins
Fold Fold fold	a.28 — Acyl carrier protein-like
Superfamily Superfamily superfamily	a.28.1 — ACP-like
Family Family family	a.28.1.1 — Acyl-carrier protein (ACP)

Domain ID domain_id	d3ejee3
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d3ejef_
Class class	a — All alpha proteins
Fold Fold fold	a.104 — Cytochrome P450
Superfamily Superfamily superfamily	a.104.1 — Cytochrome P450
Family Family family	a.104.1.0 — automated matches

Domain ID domain_id	d3ejeg2
Class class	a — All alpha proteins
Fold Fold fold	a.28 — Acyl carrier protein-like
Superfamily Superfamily superfamily	a.28.1 — ACP-like
Family Family family	a.28.1.1 — Acyl-carrier protein (ACP)

Domain ID domain_id	d3ejeg3
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d3ejeh_
Class class	a — All alpha proteins
Fold Fold fold	a.104 — Cytochrome P450
Superfamily Superfamily superfamily	a.104.1 — Cytochrome P450
Family Family family	a.104.1.0 — automated matches

CATH v4.4 (12 domains)

Domain ID domain_id	3ejeA00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	1200 — Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A
Homologous superfamily homologous superfamily	10 — ACP-like

Domain ID domain_id	3ejeB01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	43 — Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase; domain 2
Homologous superfamily homologous superfamily	20 —

Domain ID domain_id	3ejeB02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	630 — Cytochrome p450
Homologous superfamily homologous superfamily	10 — Cytochrome P450

Domain ID domain_id	3ejeC00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	1200 — Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A
Homologous superfamily homologous superfamily	10 — ACP-like

Domain ID domain_id	3ejeD01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	43 — Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase; domain 2
Homologous superfamily homologous superfamily	20 —

Domain ID domain_id	3ejeD02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	630 — Cytochrome p450
Homologous superfamily homologous superfamily	10 — Cytochrome P450

Domain ID domain_id	3ejeE00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	1200 — Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A
Homologous superfamily homologous superfamily	10 — ACP-like

Domain ID domain_id	3ejeF01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	43 — Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase; domain 2
Homologous superfamily homologous superfamily	20 —

Domain ID domain_id	3ejeF02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	630 — Cytochrome p450
Homologous superfamily homologous superfamily	10 — Cytochrome P450

Domain ID domain_id	3ejeG00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	1200 — Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A
Homologous superfamily homologous superfamily	10 — ACP-like

Domain ID domain_id	3ejeH01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	43 — Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase; domain 2
Homologous superfamily homologous superfamily	20 —

Domain ID domain_id	3ejeH02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	630 — Cytochrome p450
Homologous superfamily homologous superfamily	10 — Cytochrome P450

▶

Unit-cell length a length_a	61.200 Å
Unit-cell length b length_b	92.000 Å
Unit-cell length c length_c	108.000 Å
Unit-cell angle α angle_alpha	109.30 °
Unit-cell angle β angle_beta	90.80 °
Unit-cell angle γ angle_gamma	90.10 °
Molecules per unit cell Z z_pdb	4

Space group space_group	P 1
Space-group number int_tables_number	1
Crystal system crystal_system	—

Resolution resolution	2.100 Å
Low-resolution limit resolution_low	19.950 Å
R factor r_factor	0.2422
R_work r_work	0.2405
R_free r_free	0.2743

Crystal Structure of P450BioI in complex with octadec-9Z-enoic acid ligated Acyl Carrier Protein

1. Protein Identity and Related Structures Protein Identity & Related Structures

Acyl carrier protein

State in the Current Structure

Other States of the Same Protein in the Database

Biotin biosynthesis cytochrome P450-like enzyme

State in the Current Structure

Other States of the Same Protein in the Database

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

3eje__assembly_2__model_1

3eje__assembly_2__model_1 | I(q)

3eje__assembly_2__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

6. Fold Classification (SCOP + CATH) 24 domains

SCOP 2.08 (12 domains)

CATH v4.4 (12 domains)

7. Citations (1)

Crystal Structure of P450BioI in complex with octadec-9Z-enoic acid ligated Acyl Carrier Protein

1. Protein Identity and Related Structures Protein Identity & Related Structures

Acyl carrier protein

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Biotin biosynthesis cytochrome P450-like enzyme

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

3eje__assembly_2__model_1

3eje__assembly_2__model_1 | I(q)

3eje__assembly_2__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

6. Fold Classification (SCOP + CATH) 24 domains

SCOP 2.08 (12 domains)

CATH v4.4 (12 domains)

7. Citations (1)