SAXSdb — 6o6e

▼

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

L-proline--[L-prolyl-carrier protein] ligase

Pseudomonas protegens Pf-5

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	Peptidyl carrier protein PltL × 1 （Q4KCZ1） FORMIC ACID × 13 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1 MALONIC ACID × 2 ;5'-deoxy-5'-({(2S)-2-({2-[(N-{(2R)-4-[(dioxo-lambda~5~-phosphanyl)oxy]-2-hydroxy-3,3-dimethylbutanoyl}-beta-alanyl)amino]ethyl}sulfanyl)-2-[(2S)-pyrrolidin-2-yl]ethanesulfonyl}amino)adenosine ; × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	PLTF_PSEF5
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain B； PDBConstruct 1–498； UniProt 1–498

Peptidyl carrier protein PltL

Pseudomonas protegens Pf-5

UniProt Q4KCZ1

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	L-proline--[L-prolyl-carrier protein] ligase × 1 （Q4KCY5） FORMIC ACID × 13 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1 MALONIC ACID × 2 ;5'-deoxy-5'-({(2S)-2-({2-[(N-{(2R)-4-[(dioxo-lambda~5~-phosphanyl)oxy]-2-hydroxy-3,3-dimethylbutanoyl}-beta-alanyl)amino]ethyl}sulfanyl)-2-[(2S)-pyrrolidin-2-yl]ethanesulfonyl}amino)adenosine ; × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q4KCZ1_PSEF5
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain E； PDBConstruct 1–86； UniProt 1–86

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	6o6e
Deposition date deposition_date	2019-03-06
Structure title title	Crystal structure of PltF trapped with PltL using a proline adenosine vinylsulfonamide inhibitor
Keywords keywords	nonribosomal peptide synthetase, NRPS, type II, biosynthesis, pyoluteorin, Ligase-Transport protein complex; Ligase/Transport protein
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.

6o6e__assembly_1__model_1

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

Download this curve (.dat)

6o6e__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

6o6e__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	25.02 Å
Rg (electron density)	23.72 Å
Total Rg	24.58 Å
Atom count	4448
Residues	578
Excluded volume	79249 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`6o6e__assembly_1__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 (7)

Entity 1 Entity 1 polymer

Description description	L-proline--[L-prolyl-carrier protein] ligase
Molecular weight formula_weight	56397.7 kDa
EC 编号 ec_number	6.2.1.53
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B
Atom count atom_count	4552

MKLLHERMMHSLARYPRQTAVVDEQDALSYEALELRIREFVAMLCALGVGQGQRILLWAHKSVDLVAVMQAALRLGVVYVPVDPLSPVSRLEKIAGDSQAVLVLCTAARLEELAGSALAQVRSVVLDDPASAGYWRNIDTGSSVVPTLAIQPDDLAYILYTSGSTGVPKGVALSHGNALAFVDWACERYCFQPGERFANHAPLHFDLSVLDIYCALNVGATVCLVPESIAFSPRLLTDFIRQHEISIWYSVPSVLMMMMQDGDLLSDIQDTLRVLLFAGEPFPVKHLRDLRAAYADVRLANLFGPTETNVCTAFEVGAIDPERVLPVPIGTAASGNQVWAQKPDGSRCAVGEEGELVVQGPTVMLGYFAKPAQEGPYKTGDMVRQRPDGNYEYLGRRDDMLKVRGNRIERGEVEAALLAHPQVSEAAVLVVGEGMNAQLWGVLVAHTRDALSLIDLKRHCAQRLPRYMIIDKVLCLDALPRNANGKVDRFALARQVEGKLAAALEHHHHHHHH

Source Source

Source organism organism	Pseudomonas protegens Pf-5
NCBI taxonomy ID ncbi_taxonomy_id	220664
Host organism host_organism	Escherichia coli BL21

Entity 2 Entity 2 polymer

Description description	Peptidyl carrier protein PltL
Molecular weight formula_weight	11141.7 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	E

MDGEEVKEKIRRYIMEDLIGPSAKEDELDDQTPLLEWGILNSMNIVKLMVYIRDEMGVSIPSTHITGKYFKDLNAISRTVEQLKAESALEHHHHHH

Source Source

Source organism organism	Pseudomonas protegens Pf-5
NCBI taxonomy ID ncbi_taxonomy_id	220664
Host organism host_organism	Escherichia coli BL21

Entity 3 Entity 3 non-polymer

Description description	FORMIC ACID
Molecular weight formula_weight	46.0 kDa
Source method src_method	syn
Copy count entity_count	13

Entity 4 Entity 4 non-polymer

Description description	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
Molecular weight formula_weight	122.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 non-polymer

Description description	MALONIC ACID
Molecular weight formula_weight	104.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 6 Entity 6 non-polymer

Description description	;5'-deoxy-5'-({(2S)-2-({2-[(N-{(2R)-4-[(dioxo-lambda~5~-phosphanyl)oxy]-2-hydroxy-3,3-dimethylbutanoyl}-beta-alanyl)amino]ethyl}sulfanyl)-2-[(2S)-pyrrolidin-2-yl]ethanesulfonyl}amino)adenosine ;
Molecular weight formula_weight	765.8 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 7 Entity 7 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	104

▼

6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d6o6eb1
Class class	e — Multi-domain proteins (alpha and beta)
Fold Fold fold	e.23 — Acetyl-CoA synthetase-like
Superfamily Superfamily superfamily	e.23.1 — Acetyl-CoA synthetase-like
Family Family family	e.23.1.0 — automated matches

Domain ID domain_id	d6o6eb2
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

CATH v4.4 (2 domains)

Domain ID domain_id	6o6eB02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	300 — GMP Synthetase; Chain A, domain 3
Homologous superfamily homologous superfamily	30 — ANL, C-terminal domain

Domain ID domain_id	6o6eE00
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

▶

Unit-cell length a length_a	170.550 Å
Unit-cell length b length_b	170.550 Å
Unit-cell length c length_c	64.900 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	6

Space group space_group	P 32 2 1
Space-group number int_tables_number	154
Crystal system crystal_system	—

Resolution resolution	2.140 Å
Low-resolution limit resolution_low	85.420 Å
R factor r_factor	0.2165
R_work r_work	0.2142
R_free r_free	0.2601

Crystal structure of PltF trapped with PltL using a proline adenosine vinylsulfonamide inhibitor

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

L-proline--[L-prolyl-carrier protein] ligase

State in the Current Structure

Other States of the Same Protein in the Database

Peptidyl carrier protein PltL

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

6o6e__assembly_1__model_1

6o6e__assembly_1__model_1 | I(q)

6o6e__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 (7)

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 non-polymer

Entity 7 Entity 7 water

6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)

Crystal structure of PltF trapped with PltL using a proline adenosine vinylsulfonamide inhibitor

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

L-proline--[L-prolyl-carrier protein] ligase

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Peptidyl carrier protein PltL

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

6o6e__assembly_1__model_1

6o6e__assembly_1__model_1 | I(q)

6o6e__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 (7)

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 non-polymer

Entity 7 Entity 7 water

6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)