SAXSdb — 2j3m

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

PROLYL-TRNA SYNTHETASE

ENTEROCOCCUS FAECALIS

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	ADENOSINE-5'-TRIPHOSPHATE × 2 PYRROLIDINE-2-CARBALDEHYDE × 2 MANGANESE (II) ION × 6 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q831W7_ENTFA
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–572； UniProt 1–572 Author chain B； PDBConstruct 1–572； UniProt 1–572

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	2j3m
Deposition date deposition_date	2006-08-22
Structure title title	PROLYL-TRNA SYNTHETASE FROM ENTEROCOCCUS FAECALIS COMPLEXED WITH ATP, manganese and prolinol
Keywords keywords	;BACTERIAL-TYPE PROLYL-TRNA SYNTHETASE, CLASS II AMINOACYL-TRNA SYNTHETASE, EDITING, TRANSLATION, ATP + L-PROLINE + TRNA (PRO) GIVES AMP + PPI + L-PROLYL-TRNA(PRO), 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.

2j3m__assembly_1__model_1

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

Download this curve (.dat)

2j3m__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2j3m__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	35.57 Å
Rg (electron density)	35.23 Å
Total Rg	35.40 Å
Atom count	8873
Residues	1112
Excluded volume	157550 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2j3m__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	PROLYL-TRNA SYNTHETASE
Molecular weight formula_weight	64341.6 kDa
EC 编号 ec_number	6.1.1.15
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	9247

MKQSKMLIPTLREVPNDAEVLSHQILLRAGYIRQVAAGIYSYLPLANRVLEKLKTIMREEFEKIDAVEMLMPALLPAELWKESGRYETYGPNLYRLKDRNDRDYILGPTHEETFTELIRDEINSYKRLPLNLYQIQTKYRDEKRSRSGLLRGREFIMKDGYSFHADEASLDQSYRDYEKAYSRIFERCGLEFRAIIGDGGAMGGKDSKEFMAISEIGEDTICYSTESDYAANLEMATSLYTPKKSHETQLDLEKIATPEVGTIAEVANFFEVEPQRIIKSVLFIADEEPVMVLVRGDHDVNDVKLKNFLGADFLDEATEEDARRVLGAGFGSIGPVNVSEDVKIYADLAVQDLANAIVGANEDGYHLTNVNPDRDFQPISYEDLRFVQEGDPSPDGNGVLAFTKGIEIGHIFKLGTRYSDAMGATVLDENGREKSVIMGCYGIGVSRLLSAIVEQNADERGINWPTGIAPFDLHVVQMNVKDEYQTKLSQEVEAMMTEAGYEVLVDDRNERAGVKFADADLIGCPIRITVGKKAVDGVVEVKIKRTGEMLEVRKEELESTLSILMNTTSEVE

Source Source

Source organism organism	ENTEROCOCCUS FAECALIS
NCBI taxonomy ID ncbi_taxonomy_id	1351
Host organism host_organism	ESCHERICHIA COLI

Entity 2 Entity 2 non-polymer

Description description	ADENOSINE-5'-TRIPHOSPHATE
Molecular weight formula_weight	507.2 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 non-polymer

Description description	PYRROLIDINE-2-CARBALDEHYDE
Molecular weight formula_weight	99.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 non-polymer

Description description	MANGANESE (II) ION
Molecular weight formula_weight	54.9 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	363

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6. Fold Classification (SCOP + CATH) 6 domains

CATH v4.4 (6 domains)

Domain ID domain_id	2j3mA01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	800 — Anticodon-binding domain

Domain ID domain_id	2j3mA02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	930 — BirA Bifunctional Protein; domain 2
Homologous superfamily homologous superfamily	10 — Bira Bifunctional Protein; Domain 2

Domain ID domain_id	2j3mA03
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	960 — YbaK protein
Homologous superfamily homologous superfamily	10 — YbaK/aminoacyl-tRNA synthetase-associated domain

Domain ID domain_id	2j3mB01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	800 — Anticodon-binding domain

Domain ID domain_id	2j3mB02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	930 — BirA Bifunctional Protein; domain 2
Homologous superfamily homologous superfamily	10 — Bira Bifunctional Protein; Domain 2

Domain ID domain_id	2j3mB03
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	960 — YbaK protein
Homologous superfamily homologous superfamily	10 — YbaK/aminoacyl-tRNA synthetase-associated domain

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Unit-cell length a length_a	68.583 Å
Unit-cell length b length_b	92.679 Å
Unit-cell length c length_c	101.223 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	106.11 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	2.300 Å
Low-resolution limit resolution_low	29.490 Å
R factor r_factor	0.1980
R_work r_work	0.1960
R_free r_free	0.2600

PROLYL-TRNA SYNTHETASE FROM ENTEROCOCCUS FAECALIS COMPLEXED WITH ATP, manganese and prolinol

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

PROLYL-TRNA SYNTHETASE

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

2j3m__assembly_1__model_1

2j3m__assembly_1__model_1 | I(q)

2j3m__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 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 6 domains

CATH v4.4 (6 domains)

7. Citations (1)

PROLYL-TRNA SYNTHETASE FROM ENTEROCOCCUS FAECALIS COMPLEXED WITH ATP, manganese and prolinol

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

PROLYL-TRNA SYNTHETASE

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

2j3m__assembly_1__model_1

2j3m__assembly_1__model_1 | I(q)

2j3m__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 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 6 domains

CATH v4.4 (6 domains)

7. Citations (1)