SAXSdb — 1nj6

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

Proline-tRNA Synthetase

Methanothermobacter thermautotrophicus

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	ZINC ION × 2 MAGNESIUM ION × 2 '5'-O-(N-(L-ALANYL)-SULFAMOYL)ADENOSINE × 2 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	SYP_METTH
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 21–501； UniProt 1–481

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	1nj6
Deposition date deposition_date	2002-12-30
Structure title title	Crystal structure of Prolyl-tRNA Synthetase from Methanothermobacter thermautotrophicus bound to alanine sulfamoyl adenylate
Keywords keywords	Protein-Aminoacyladenylate Complex Class-II 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.

1nj6__assembly_1__model_1

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

Download this curve (.dat)

1nj6__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1nj6__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	31.40 Å
Rg (electron density)	30.11 Å
Total Rg	30.96 Å
Atom count	7624
Residues	926
Excluded volume	135160 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1nj6__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	Proline-tRNA Synthetase
Molecular weight formula_weight	58170.3 kDa
EC 编号 ec_number	6.1.1.15
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	3838

MGSSHHHHHHSSGLVPRGSHMQKPIKKDPNRYHGEKMTEFSEWFHNILEEAEIIDQRYPVKGMHVWMPHGFMIRKNTLKILRRILDRDHEEVLFPLLVPEDELAKEAIHVKGFEDEVYWVTHGGLSKLQRKLALRPTSETVMYPMFALWVRSHTDLPMRFYQVVNTFRYETKHTRPLIRVREITTFKEAHTIHATASEAEEQVERAVEIYKEFFNSLGIPYLITRRPPWDKFPGSEYTVAFDTLMPDGKTLQIGTVHNLGQTFARTFEIKFETPEGDHEYVHQTCYGLSDRVIASVIAIHGDESGLCLPPDVAAHQVVIVPIIFKKAAEEVMEACRELRSRLEAAGFRVHLDDRDIRAGRKYYEWEMRGVPLRVEIGPRDLEKGAAVISRRDTGEKVTADLQGIEETLRELMKDILENLRTRAWERMESEIREAETLEEASRIVDEKRGIISFMWCGEEECGMDVEEKVRVDILGIQEEGSGTCINCGREAPYRAYLARTY

Source Source

Source organism organism	Methanothermobacter thermautotrophicus
NCBI taxonomy ID ncbi_taxonomy_id	187420
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	'5'-O-(N-(L-ALANYL)-SULFAMOYL)ADENOSINE
Molecular weight formula_weight	417.4 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	26

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6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (3 domains)

Domain ID domain_id	d1nj6a1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.51 — Anticodon-binding domain-like
Superfamily Superfamily superfamily	c.51.1 — Class II aaRS ABD-related
Family Family family	c.51.1.1 — Anticodon-binding domain of Class II aaRS

Domain ID domain_id	d1nj6a2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.68 — IF3-like
Superfamily Superfamily superfamily	d.68.5 — C-terminal domain of ProRS
Family Family family	d.68.5.1 — C-terminal domain of ProRS

Domain ID domain_id	d1nj6a3
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.104 — Class II aaRS and biotin synthetases
Superfamily Superfamily superfamily	d.104.1 — Class II aaRS and biotin synthetases
Family Family family	d.104.1.1 — Class II aminoacyl-tRNA synthetase (aaRS)-like, catalytic domain

CATH v4.4 (3 domains)

Domain ID domain_id	1nj6A01
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	1nj6A02
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	1nj6A03
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	110 — Translation Initiation Factor IF3
Homologous superfamily homologous superfamily	30 — C-terminal domain of ProRS

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Unit-cell length a length_a	143.539 Å
Unit-cell length b length_b	143.539 Å
Unit-cell length c length_c	164.178 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	12

Space group space_group	P 65 2 2
Space-group number int_tables_number	179
Crystal system crystal_system	—

Resolution resolution	2.850 Å
Low-resolution limit resolution_low	29.160 Å
R factor r_factor	0.2230
R_work r_work	0.2230
R_free r_free	0.2560

Crystal structure of Prolyl-tRNA Synthetase from Methanothermobacter thermautotrophicus bound to alanine sulfamoyl adenylate

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

Proline-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

1nj6__assembly_1__model_1

1nj6__assembly_1__model_1 | I(q)

1nj6__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

SCOP 2.08 (3 domains)

CATH v4.4 (3 domains)

7. Citations (1)

Crystal structure of Prolyl-tRNA Synthetase from Methanothermobacter thermautotrophicus bound to alanine sulfamoyl adenylate

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

Proline-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

1nj6__assembly_1__model_1

1nj6__assembly_1__model_1 | I(q)

1nj6__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

SCOP 2.08 (3 domains)

CATH v4.4 (3 domains)

7. Citations (1)