3etc

2.1 A structure of acyl-adenylate synthetase from Methanosarcina acetivorans containing a link between Lys256 and Cys298

Method: X-RAY DIFFRACTION

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

AMP-binding protein

Methanosarcina acetivorans

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	FORMYL GROUP × 2 TRIETHYLENE GLYCOL × 3 PENTAETHYLENE GLYCOL × 2 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 3 MAGNESIUM ION × 2 NITRATE ION × 2 GLYCEROL × 7 water × 2	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	FORMYL GROUP × 1 TRIETHYLENE GLYCOL × 1 PENTAETHYLENE GLYCOL × 2 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 2 MAGNESIUM ION × 1 NITRATE ION × 1 GLYCEROL × 4 water × 1	Consistent with protein count
3	Protein monomer	Monomer	Protein 1	FORMYL GROUP × 1 TRIETHYLENE GLYCOL × 2 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 1 MAGNESIUM ION × 1 NITRATE ION × 1 GLYCEROL × 3 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q8TLW1_METAC
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 24–580； UniProt 4–560 Author chain B； PDBConstruct 24–580； UniProt 4–560

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	3etc
Deposition date deposition_date	2008-10-07
Structure title title	2.1 A structure of acyl-adenylate synthetase from Methanosarcina acetivorans containing a link between Lys256 and Cys298
Keywords keywords	Adenylate-forming Acyl-CoA synthetase Ligase, 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.

3etc__assembly_3__model_1

Assembly 3 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

3etc__assembly_3__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3etc__assembly_3__model_1 | P(r) · Pending

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

Rg（Guinier）	24.00 Å
Rg (electron density)	22.80 Å
Total Rg	23.70 Å
Atom count	4282
Residues	537
Excluded volume	76531 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3etc__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`3etc__assembly_2__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`3etc__assembly_3__model_1`	monomeric （1）	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 (9)

Entity 1 Entity 1 polymer

Description description	AMP-binding protein
Molecular weight formula_weight	66230.9 kDa
EC 编号 ec_number	6.2.1.-
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	9016

MGHHHHHHHHHHSSGHIDDDDKHMTSLLSQFVSKTDFESYEDFQENFKILVPENFNFAYDVVDVYARDSPEKLAMIWCDDYGNEKIFTFKDLKYYSDKAANFFVKHGIGKGDYVMLTLKSRYDFWYCMLGLHKLGAIAVPATHMLKTRDIVYRIEKAGLKMIVCIAEDDVPEQVDEAHAECGDIPLKKAKVGGDVLEGWIDFRKELEESSPIFERPTGEVSTKNEDICLVYFSSGTAGFPKMVEHDNTYPLGHILTAKYWQNVEDDGLHYTVADSGWGKCVWGKLYGQWIAGCAVFVYDYDRFEAKNMLEKASKYGVTTFCAPPTIYRFLIKEDLSHYNFSTLKYAVVAGEPLNPEVFNRFLEFTGIKLMEGFGQTETVVTIATFPWMEPKPGSIGKPTPGYKIELMDRDGRLCEVGEEGEIVINTMEGKPVGLFVHYGKDPERTEETWHDGYYHTGDMAWMDEDGYLWFVGRADDIIKTSGYKVGPFEVESALIQHPAVLECAITGVPDPVRGQVIKATIVLTKDYTPSDSLKNELQDHVKNVTAPYKYPRIIEFVPELPKTISGKIRRVEIRDKDQSQ

Source Source

Source organism organism	Methanosarcina acetivorans
NCBI taxonomy ID ncbi_taxonomy_id	2214
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	FORMYL GROUP
Molecular weight formula_weight	30.0 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 non-polymer

Description description	TRIETHYLENE GLYCOL
Molecular weight formula_weight	150.2 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 4 Entity 4 non-polymer

Description description	PENTAETHYLENE GLYCOL
Molecular weight formula_weight	238.3 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 non-polymer

Description description	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
Molecular weight formula_weight	238.3 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 6 Entity 6 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 7 Entity 7 non-polymer

Description description	NITRATE ION
Molecular weight formula_weight	62.0 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 8 Entity 8 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	7

Entity 9 Entity 9 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	429

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6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id	3etcA01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	12780 — ANL, N-terminal domain

Domain ID domain_id	3etcA02
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	3etcB01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	12780 — ANL, N-terminal domain

Domain ID domain_id	3etcB02
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

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Unit-cell length a length_a	91.699 Å
Unit-cell length b length_b	96.371 Å
Unit-cell length c length_c	141.543 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	2.100 Å
Low-resolution limit resolution_low	29.880 Å
R factor r_factor	0.1768
R_work r_work	0.1752
R_free r_free	0.2065

2.1 A structure of acyl-adenylate synthetase from Methanosarcina acetivorans containing a link between Lys256 and Cys298

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

AMP-binding protein

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

3etc__assembly_3__model_1

3etc__assembly_3__model_1 | I(q)

3etc__assembly_3__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 (9)

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 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 non-polymer

Entity 9 Entity 9 water

6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

7. Citations (1)

2.1 A structure of acyl-adenylate synthetase from Methanosarcina acetivorans containing a link between Lys256 and Cys298

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

AMP-binding protein

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

3etc__assembly_3__model_1

3etc__assembly_3__model_1 | I(q)

3etc__assembly_3__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 (9)

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 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 non-polymer

Entity 9 Entity 9 water

6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

7. Citations (1)