SAXSdb — 5ja1

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

Enterobactin synthase component F

Escherichia coli (strain K12)

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	Enterobactin biosynthesis protein YbdZ × 1 （P18393） ;5'-({[(2R,3S)-3-amino-4-hydroxy-2-{[2-({N-[(2R)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alanyl}amino)ethyl]sulfanyl}butyl]sulfonyl}amino)-5'-deoxyadenosine ; × 1 CHLORIDE ION × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	ENTF_ECOLI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 3–1295； UniProt 1–1293

Enterobactin biosynthesis protein YbdZ

Escherichia coli (strain K12)

UniProt P18393

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	Enterobactin synthase component F × 1 （P11454） ;5'-({[(2R,3S)-3-amino-4-hydroxy-2-{[2-({N-[(2R)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alanyl}amino)ethyl]sulfanyl}butyl]sulfonyl}amino)-5'-deoxyadenosine ; × 1 CHLORIDE ION × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	YBDZ_ECOLI
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 3–74； UniProt 1–72

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.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	5ja1
Deposition date deposition_date	2016-04-11
Structure title title	EntF, a Terminal Nonribosomal Peptide Synthetase Module Bound to the MbtH-Like Protein YbdZ
Keywords keywords	;NONRIBOSOMAL PEPTIDE SYNTHETASE, NRPS, CONDENSATION, ADENYLATION, PCP, THIOESTERASE, MBTH-LIKE PROTEIN, PHOSPHOPANTETHEINE, BIOSYNTHETIC PROTEIN, LIGASE ;; LIGASE
Experimental Method method	X-RAY DIFFRACTION

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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.

5ja1__assembly_1__model_1

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

Download this curve (.dat)

5ja1__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

5ja1__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	41.36 Å
Rg (electron density)	41.63 Å
Total Rg	41.52 Å
Atom count	9827
Residues	1297
Excluded volume	174700 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`5ja1__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download

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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	Enterobactin synthase component F
Molecular weight formula_weight	142313.3 kDa
EC 编号 ec_number	2.7.7.-
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	9892

GHMSQHLPLVAAQPGIWMAEKLSELPSAWSVAHYVELTGEVDSPLLARAVVAGLAQADTLRMRFTEDNGEVWQWVDDALTFELPEIIDLRTNIDPHGTAQALMQADLQQDLRVDSGKPLVFHQLIQVADNRWYWYQRYHHLLVDGFSFPAITRQIANIYCTWLRGEPTPASPFTPFADVVEEYQQYRESEAWQRDAAFWAEQRRQLPPPASLSPAPLPGRSASADILRLKLEFTDGEFRQLATQLSGVQRTDLALALAALWLGRLCNRMDYAAGFIFMRRLGSAALTATGPVLNVLPLGIHIAAQETLPELATRLAAQLKKMRRHQRYDAEQIVRDSGRAAGDEPLFGPVLNIKVFDYQLDIPDVQAQTHTLATGPVNDLELALFPDVHGDLSIEILANKQRYDEPTLIQHAERLKMLIAQFAADPALLCGDVDIMLPGEYAQLAQLNATQVEIPETTLSALVAEQAAKTPDAPALADARYLFSYREMREQVVALANLLRERGVKPGDSVAVALPRSVFLTLALHAIVEAGAAWLPLDTGYPDDRLKMMLEDARPSLLITTDDQLPRFSDVPNLTSLCYNAPLTPQGSAPLQLSQPHHTAYIIFTSGSTGRPKGVMVGQTAIVNRLLWMQNHYPLTGEDVVAQKTPCSFDVSVWEFFWPFIAGAKLVMAEPEAHRDPLAMQQFFAEYGVTTTHFVPSMLAAFVASLTPQTARQSCATLKQVFCSGEALPADLCREWQQLTGAPLHNLYGPTEAAVDVSWYPAFGEELAQVRGSSVPIGYPVWNTGLRILDAMMHPVPPGVAGDLYLTGIQLAQGYLGRPDLTASRFIADPFAPGERMYRTGDVARWLDNGAVEYLGRSDDQLKIRGQRIELGEIDRVMQALPDVEQAVTHACVINQAAATGGDARQLVGYLVSQSGLPLDTSALQAQLRETLPPHMVPVVLLQLPQLPLSANGKLDRKALPLPELKAQAPGRAPKAGSETIIAAAFSSLLGCDVQDADADFFALGGHSLLAMKLAAQLSRQVARQVTPGQVMVASTVAKLATIIDAEEDSTRRMGFETILPLREGNGPTLFCFHPASGFAWQFSVLSRYLDPQWSIIGIQSPRPNGPMQTAANLDEVCEAHLATLLEQQPHGPYYLLGYSLGGTLAQGIAARLRARGEQVAFLGLLDTWPPETQNWQEKEANGLDPEVLAEINREREAFLAAQQGSTSTELFTTIEGNYADAVRLLTTAHSVPFDGKATLFVAERTLQEGMSPERAWSPWIAELDIYRQDCAHVDIISPGTFEKIGPIIRATLNR

Source Source

Source organism organism	Escherichia coli (strain K12)
NCBI taxonomy ID ncbi_taxonomy_id	83333
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 polymer

Description description	Enterobactin biosynthesis protein YbdZ
Molecular weight formula_weight	8469.4 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

GHMAFSNPFDDPQGAFYILRNAQGQFSLWPQQCVLPAGWDIVCQPQSQASCQQWLEAHWRTLTPTNFTQLQEAQ

Source Source

Source organism organism	Escherichia coli (strain K12)
NCBI taxonomy ID ncbi_taxonomy_id	83333
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 3 Entity 3 non-polymer

Description description	;5'-({[(2R,3S)-3-amino-4-hydroxy-2-{[2-({N-[(2R)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alanyl}amino)ethyl]sulfanyl}butyl]sulfonyl}amino)-5'-deoxyadenosine ;
Molecular weight formula_weight	773.8 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	49

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6. Fold Classification (SCOP + CATH) 5 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d5ja1b_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.100 — MbtH/L9 domain-like
Superfamily Superfamily superfamily	d.100.2 — MbtH-like
Family Family family	d.100.2.0 — automated matches

CATH v4.4 (4 domains)

Domain ID domain_id	5ja1A01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	559 — Chloramphenicol Acetyltransferase
Homologous superfamily homologous superfamily	10 — Chloramphenicol acetyltransferase-like domain

Domain ID domain_id	5ja1A02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	559 — Chloramphenicol Acetyltransferase
Homologous superfamily homologous superfamily	30 — Nonribosomal peptide synthetase, condensation domain

Domain ID domain_id	5ja1A03
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1820 — Alpha/Beta hydrolase fold, catalytic domain

Domain ID domain_id	5ja1B00
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	820 — Rubredoxin-like
Homologous superfamily homologous superfamily	10 — Structural Genomics, Unknown Function 30-nov-00 1gh9 Mol_id

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Unit-cell length a length_a	161.185 Å
Unit-cell length b length_b	57.679 Å
Unit-cell length c length_c	183.945 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	97.93 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	I 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	3.000 Å
Low-resolution limit resolution_low	56.308 Å
R factor r_factor	0.1879
R_work r_work	0.1854
R_free r_free	0.2349

EntF, a Terminal Nonribosomal Peptide Synthetase Module Bound to the MbtH-Like Protein YbdZ

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

Enterobactin synthase component F

State in the Current Structure

Other States of the Same Protein in the Database

Enterobactin biosynthesis protein YbdZ

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

5ja1__assembly_1__model_1

5ja1__assembly_1__model_1 | I(q)

5ja1__assembly_1__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 (5)

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 water

6. Fold Classification (SCOP + CATH) 5 domains

SCOP 2.08 (1 domains)

CATH v4.4 (4 domains)

7. Citations (2)

EntF, a Terminal Nonribosomal Peptide Synthetase Module Bound to the MbtH-Like Protein YbdZ

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

Enterobactin synthase component F

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Enterobactin biosynthesis protein YbdZ

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

5ja1__assembly_1__model_1

5ja1__assembly_1__model_1 | I(q)

5ja1__assembly_1__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 (5)

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 water

6. Fold Classification (SCOP + CATH) 5 domains

SCOP 2.08 (1 domains)

CATH v4.4 (4 domains)

7. Citations (2)