SAXSdb — 5t3d

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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 monomer	Monomer	Protein 1	;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 water × 1	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

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	5t3d
Deposition date deposition_date	2016-08-25
Structure title title	Crystal structure of holo-EntF a nonribosomal peptide synthetase in the thioester-forming conformation
Keywords keywords	Nonribosomal peptide synthetase, NRPS, Condensation, Adenylation, PCP, Thioesterase, phosphopantetheine, BIOSYNTHETIC PROTEIN; BIOSYNTHETIC PROTEIN
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.

5t3d__assembly_1__model_1

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

Download this curve (.dat)

5t3d__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

5t3d__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	35.12 Å
Rg (electron density)	34.81 Å
Total Rg	35.13 Å
Atom count	7852
Residues	1042
Excluded volume	139650 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`5t3d__assembly_1__model_1`	monomeric （1）	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 (3)

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	7865

GHMSQHLPLVAAQPGIWMAEKLSELPSAWSVAHYVELTGEVDSPLLARAVVAGLAQADTLRMRFTEDNGEVWQWVDDALTFELPEIIDLRTNIDPHGTAQALMQADLQQDLRVDSGKPLVFHQLIQVADNRWYWYQRYHHLLVDGFSFPAITRQIANIYCTWLRGEPTPASPFTPFADVVEEYQQYRESEAWQRDAAFWAEQRRQLPPPASLSPAPLPGRSASADILRLKLEFTDGEFRQLATQLSGVQRTDLALALAALWLGRLCNRMDYAAGFIFMRRLGSAALTATGPVLNVLPLGIHIAAQETLPELATRLAAQLKKMRRHQRYDAEQIVRDSGRAAGDEPLFGPVLNIKVFDYQLDIPDVQAQTHTLATGPVNDLELALFPDVHGDLSIEILANKQRYDEPTLIQHAERLKMLIAQFAADPALLCGDVDIMLPGEYAQLAQLNATQVEIPETTLSALVAEQAAKTPDAPALADARYLFSYREMREQVVALANLLRERGVKPGDSVAVALPRSVFLTLALHAIVEAGAAWLPLDTGYPDDRLKMMLEDARPSLLITTDDQLPRFSDVPNLTSLCYNAPLTPQGSAPLQLSQPHHTAYIIFTSGSTGRPKGVMVGQTAIVNRLLWMQNHYPLTGEDVVAQKTPCSFDVSVWEFFWPFIAGAKLVMAEPEAHRDPLAMQQFFAEYGVTTTHFVPSMLAAFVASLTPQTARQSCATLKQVFCSGEALPADLCREWQQLTGAPLHNLYGPTEAAVDVSWYPAFGEELAQVRGSSVPIGYPVWNTGLRILDAMMHPVPPGVAGDLYLTGIQLAQGYLGRPDLTASRFIADPFAPGERMYRTGDVARWLDNGAVEYLGRSDDQLKIRGQRIELGEIDRVMQALPDVEQAVTHACVINQAAATGGDARQLVGYLVSQSGLPLDTSALQAQLRETLPPHMVPVVLLQLPQLPLSANGKLDRKALPLPELKAQAPGRAPKAGSETIIAAAFSSLLGCDVQDADADFFALGGHSLLAMKLAAQLSRQVARQVTPGQVMVASTVAKLATIIDAEEDSTRRMGFETILPLREGNGPTLFCFHPASGFAWQFSVLSRYLDPQWSIIGIQSPRPNGPMQTAANLDEVCEAHLATLLEQQPHGPYYLLGYSLGGTLAQGIAARLRARGEQVAFLGLLDTWPPETQNWQEKEANGLDPEVLAEINREREAFLAAQQGSTSTELFTTIEGNYADAVRLLTTAHSVPFDGKATLFVAERTLQEGMSPERAWSPWIAELDIYRQDCAHVDIISPGTFEKIGPIIRATLNR

Source Source

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

Entity 2 Entity 2 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 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	13

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6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id	5t3dA01
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	5t3dA02
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

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Unit-cell length a length_a	127.711 Å
Unit-cell length b length_b	127.711 Å
Unit-cell length c length_c	186.940 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	P 41 21 2
Space-group number int_tables_number	92
Crystal system crystal_system	—

Resolution resolution	2.800 Å
Low-resolution limit resolution_low	60.427 Å
R factor r_factor	0.1877
R_work r_work	0.1854
R_free r_free	0.2319

Crystal structure of holo-EntF a nonribosomal peptide synthetase in the thioester-forming conformation

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

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

5t3d__assembly_1__model_1

5t3d__assembly_1__model_1 | I(q)

5t3d__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

7. Citations (1)

Crystal structure of holo-EntF a nonribosomal peptide synthetase in the thioester-forming conformation

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

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

5t3d__assembly_1__model_1

5t3d__assembly_1__model_1 | I(q)

5t3d__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

7. Citations (1)