SAXSdb — 6abl

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

Pyrrolysine--tRNA ligase

Methanosarcina mazei JCM 9314

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	MAGNESIUM ION × 6 ADENOSINE-5'-TRIPHOSPHATE × 2 (2S)-2-azanyl-6-[(2-bromophenyl)methoxycarbonylamino]hexanoic acid × 2 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	PYLS_METMA
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 5–274； UniProt 185–454

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	6abl
Deposition date deposition_date	2018-07-22
Structure title title	Crystal structure of Methanosarcina mazei PylRS(Y306A/Y384F) complexed with oBrZLys
Keywords keywords	aminoacyl-tRNA synthetase, non-natural amino acids, pyrrolysyl-tRNA synthetase, tRNA, TRANSLATION; TRANSLATION
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.

6abl__assembly_1__model_1

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

Download this curve (.dat)

6abl__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

6abl__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	25.32 Å
Rg (electron density)	24.28 Å
Total Rg	25.08 Å
Atom count	4422
Residues	534
Excluded volume	78825 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`6abl__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	Pyrrolysine--tRNA ligase
Molecular weight formula_weight	31347.0 kDa
EC 编号 ec_number	6.1.1.26
Mutation mutation	Y306A, Y384F
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	2599

GSHMASAPALTKSQTDRLEVLLNPKDEISLNSGKPFRELESELLSRRKKDLQQIYAEERENYLGKLEREITRFFVDRGFLEIKSPILIPLEYIERMGIDNDTELSKQIFRVDKNFCLRPMLAPNLANYLRKLDRALPDPIKIFEIGPCYRKESDGKEHLEEFTMLNFCQMGSGCTRENLESIITDFLNHLGIDFKIVGDSCMVFGDTLDVMHGDLELSSAVVGPIPLDREWGIDKPWIGAGFGLERLLKVKHDFKNIKRAARSGSYYNGISTNL

Source Source

Source organism organism	Methanosarcina mazei JCM 9314
Common name common_name	Methanosarcina frisia
NCBI taxonomy ID ncbi_taxonomy_id	1293038
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 3 Entity 3 non-polymer

Description description	ADENOSINE-5'-TRIPHOSPHATE
Molecular weight formula_weight	507.2 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	(2S)-2-azanyl-6-[(2-bromophenyl)methoxycarbonylamino]hexanoic acid
Molecular weight formula_weight	359.2 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	312

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6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id	6ablA01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	287 — Helix Hairpins
Homologous superfamily homologous superfamily	540 — Helix hairpin bin

Domain ID domain_id	6ablA02
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

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Unit-cell length a length_a	101.671 Å
Unit-cell length b length_b	44.281 Å
Unit-cell length c length_c	72.654 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	118.43 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	1.470 Å
Low-resolution limit resolution_low	35.061 Å
R factor r_factor	0.1582
R_work r_work	0.1567
R_free r_free	0.1929

Crystal structure of Methanosarcina mazei PylRS(Y306A/Y384F) complexed with oBrZLys

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

Pyrrolysine--tRNA ligase

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

6abl__assembly_1__model_1

6abl__assembly_1__model_1 | I(q)

6abl__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) 2 domains

CATH v4.4 (2 domains)

7. Citations (1)

Crystal structure of Methanosarcina mazei PylRS(Y306A/Y384F) complexed with oBrZLys

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

Pyrrolysine--tRNA 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

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

6abl__assembly_1__model_1

6abl__assembly_1__model_1 | I(q)

6abl__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) 2 domains

CATH v4.4 (2 domains)

7. Citations (1)