3a5z

Crystal structure of Escherichia coli GenX in complex with elongation factor P

Method: X-RAY DIFFRACTION

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

Putative lysyl-tRNA synthetase

Escherichia coli

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	Elongation factor P × 2 （C3SGD7） 5'-O-[(L-LYSYLAMINO)SULFONYL]ADENOSINE × 2 water × 4	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 4	Elongation factor P × 2 （C3SGD7） 5'-O-[(L-LYSYLAMINO)SULFONYL]ADENOSINE × 2 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	C3SGA2_ECOLX
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 4–328； UniProt 11–335 Author chain C； PDBConstruct 4–328； UniProt 11–335 Author chain E； PDBConstruct 4–328； UniProt 11–335 Author chain G； PDBConstruct 4–328； UniProt 11–335

Elongation factor P

Escherichia coli

UniProt C3SGD7

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	Putative lysyl-tRNA synthetase × 2 （C3SGA2） 5'-O-[(L-LYSYLAMINO)SULFONYL]ADENOSINE × 2 water × 4	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 4	Putative lysyl-tRNA synthetase × 2 （C3SGA2） 5'-O-[(L-LYSYLAMINO)SULFONYL]ADENOSINE × 2 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	C3SGD7_ECOLX
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 4–191； UniProt 1–188 Author chain D； PDBConstruct 4–191； UniProt 1–188 Author chain F； PDBConstruct 4–191； UniProt 1–188 Author chain H； PDBConstruct 4–191； UniProt 1–188

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	3a5z
Deposition date deposition_date	2009-08-17
Structure title title	Crystal structure of Escherichia coli GenX in complex with elongation factor P
Keywords keywords	;aminoacyl-tRNA synthetase paralog, Translation, tRNA, Lysyl-tRNA synthetase, Elongation Factor, Structural Genomics, NPPSFA, National Project on Protein Structural and Functional Analyses, RIKEN Structural Genomics/Proteomics Initiative, RSGI, Aminoacyl-tRNA synthetase, 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.

3a5z__assembly_1__model_1

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

Download this curve (.dat)

3a5z__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3a5z__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	36.60 Å
Rg (electron density)	37.15 Å
Total Rg	37.17 Å
Atom count	7670
Residues	956
Excluded volume	135850 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3a5z__assembly_1__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`3a5z__assembly_2__model_1`	tetrameric （4）	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 (4)

Entity 1 Entity 1 polymer

Description description	Putative lysyl-tRNA synthetase
Molecular weight formula_weight	37299.3 kDa
EC 编号 ec_number	6.1.1.6
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	14965

GSHMSETASWQPSASIPNLLKRAAIMAEIRRFFADRGVLEVETPCMSQATVTDIHLVPFETRFVGPGHSQGMNLWLMTSPEYHMKRLLVAGCGPVFQLCRSFRNEEMGRYHNPEFTMLEWYRPHYDMYRLMNEVDDLLQQVLDCPAAESLSYQQAFLRYLEIDPLSADKTQLREVAAKLDLSNVADTEEDRDTLLQLLFTFGVEPNIGKEKPTFVYHFPASQASLAQISTEDHRVAERFEVYYKGIELANGFHELTDAREQQQRFEQDNRKRAARGLPQHPIDQNLIEALKVGMPDCSGVALGVDRLVMLALGAETLAEVIAFSVDRA

Source Source

Source organism organism	Escherichia coli
NCBI taxonomy ID ncbi_taxonomy_id	562
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Elongation factor P
Molecular weight formula_weight	20894.5 kDa
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

GSHMATYYSNDFRAGLKIMLDGEPYAVEASEFVKPGKGQAFARVKLRRLLTGTRVEKTFKSTDSAEGADVVDMNLTYLYNDGEFWHFMNNETFEQLSADAKAIGDNAKWLLDQAECIVTLWNGQPISVTPPNFVELEIVDTDPGLKGDTAGTGGKPATLSTGAVVKVPLFVQIGEVIKVDTRSGEYVSRVK

Source Source

Source organism organism	Escherichia coli
NCBI taxonomy ID ncbi_taxonomy_id	562
Host organism host_organism	Escherichia coli

Entity 3 Entity 3 non-polymer

Description description	5'-O-[(L-LYSYLAMINO)SULFONYL]ADENOSINE
Molecular weight formula_weight	474.5 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	229

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6. Fold Classification (SCOP + CATH) 15 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d3a5zb1
Class class	b — All beta proteins
Fold Fold fold	b.34 — SH3-like barrel
Superfamily Superfamily superfamily	b.34.5 — Translation proteins SH3-like domain
Family Family family	b.34.5.0 — automated matches

Domain ID domain_id	d3a5zb2
Class class	b — All beta proteins
Fold Fold fold	b.40 — OB-fold
Superfamily Superfamily superfamily	b.40.4 — Nucleic acid-binding proteins
Family Family family	b.40.4.0 — automated matches

CATH v4.4 (13 domains)

Domain ID domain_id	3a5zA00
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	3a5zB01
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	30 — SH3 type barrels.
Homologous superfamily homologous superfamily	30 —

Domain ID domain_id	3a5zB02
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homologous superfamily homologous superfamily	140 — Nucleic acid-binding proteins

Domain ID domain_id	3a5zC00
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	3a5zD01
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	30 — SH3 type barrels.
Homologous superfamily homologous superfamily	30 —

Domain ID domain_id	3a5zD02
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homologous superfamily homologous superfamily	140 — Nucleic acid-binding proteins

Domain ID domain_id	3a5zD03
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homologous superfamily homologous superfamily	140 — Nucleic acid-binding proteins

Domain ID domain_id	3a5zE00
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	3a5zF01
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	30 — SH3 type barrels.
Homologous superfamily homologous superfamily	30 —

Domain ID domain_id	3a5zG00
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	3a5zH01
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	30 — SH3 type barrels.
Homologous superfamily homologous superfamily	30 —

Domain ID domain_id	3a5zH02
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homologous superfamily homologous superfamily	140 — Nucleic acid-binding proteins

Domain ID domain_id	3a5zH03
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homologous superfamily homologous superfamily	140 — Nucleic acid-binding proteins

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Unit-cell length a length_a	105.930 Å
Unit-cell length b length_b	102.960 Å
Unit-cell length c length_c	119.940 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	99.40 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

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

Resolution resolution	2.500 Å
Low-resolution limit resolution_low	45.680 Å
R factor r_factor	0.2260
R_work r_work	0.2260
R_free r_free	0.2680

Crystal structure of Escherichia coli GenX in complex with elongation factor P

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

Putative lysyl-tRNA synthetase

State in the Current Structure

Other States of the Same Protein in the Database

Elongation factor P

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

3a5z__assembly_1__model_1

3a5z__assembly_1__model_1 | I(q)

3a5z__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 (4)

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 water

6. Fold Classification (SCOP + CATH) 15 domains

SCOP 2.08 (2 domains)

CATH v4.4 (13 domains)

7. Citations (1)

Crystal structure of Escherichia coli GenX in complex with elongation factor P

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

Putative lysyl-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

Elongation factor P

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

3a5z__assembly_1__model_1

3a5z__assembly_1__model_1 | I(q)

3a5z__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 (4)

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 water

6. Fold Classification (SCOP + CATH) 15 domains

SCOP 2.08 (2 domains)

CATH v4.4 (13 domains)

7. Citations (1)