SAXSdb — 8wkd

▼

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

DUF2121 domain-containing protein

Methanosarcina mazei

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	Tetrahydromethanopterin S-methyltransferase subunit A × 1 （O59640） water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	A0A0F8NKN3_METMZ
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–192； UniProt 3–193

Tetrahydromethanopterin S-methyltransferase subunit A

OrganismNot specified

UniProt O59640

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	DUF2121 domain-containing protein × 1 （A0A0F8NKN3） water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	MTRA_METMA
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain C； PDBConstruct 1–20； UniProt 148–167

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	8wkd
Deposition date deposition_date	2023-09-27
Structure title title	Connectase T1A C192S mutant from Methanocaldococcus mazei with peptide substrate
Keywords keywords	methanogenic archea, proteasome, protein ligation, transpeptidase, LIGASE; LIGASE
Experimental Method method	X-RAY DIFFRACTION

▼

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.

8wkd__assembly_1__model_1

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

Download this curve (.dat)

8wkd__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

8wkd__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	18.18 Å
Rg (electron density)	17.16 Å
Total Rg	18.13 Å
Atom count	1591
Residues	209
Excluded volume	28550 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`8wkd__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download

▶

4. Crystallography and Experiment 4. Crystallography & Experiment

▶

5. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	DUF2121 domain-containing protein
Molecular weight formula_weight	21084.2 kDa
Mutation mutation	C192S
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	1664

ALVIAFIGKNGAVMAGDMREITFEGEKPDREKLEKELYSGSIVTDEEMQKKAEEFGVKITVADCKEKVSERNGVLVGEVSSAEGGVVKKRRLYASAGNFAIAELINTEMTLTSQGKGSNFIAFGNEFTKQVANKCFKDNWTKKSNLQDAVKILILCMETVARKTASVSKQFMIVQTASNADVLKVVEKDRNS

Source Source

Source organism organism	Methanosarcina mazei
NCBI taxonomy ID ncbi_taxonomy_id	2209
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Tetrahydromethanopterin S-methyltransferase subunit A
Molecular weight formula_weight	2110.4 kDa
EC 编号 ec_number	2.1.1.86
Mutation mutation	F11V,D14K
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C

RELASKDPGAVDAKPLVVEI

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	73

▶

Unit-cell length a length_a	54.100 Å
Unit-cell length b length_b	100.970 Å
Unit-cell length c length_c	32.600 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	4

Space group space_group	P 21 21 2
Space-group number int_tables_number	18
Crystal system crystal_system	—

Resolution resolution	1.980 Å
Low-resolution limit resolution_low	47.690 Å
R factor r_factor	0.2209
R_work r_work	0.2182
R_free r_free	0.2693

Connectase T1A C192S mutant from Methanocaldococcus mazei with peptide substrate

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

DUF2121 domain-containing protein

State in the Current Structure

Other States of the Same Protein in the Database

Tetrahydromethanopterin S-methyltransferase subunit A

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

8wkd__assembly_1__model_1

8wkd__assembly_1__model_1 | I(q)

8wkd__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 water

7. Citations (1)

Connectase T1A C192S mutant from Methanocaldococcus mazei with peptide substrate

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

DUF2121 domain-containing 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

Tetrahydromethanopterin S-methyltransferase subunit A

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

8wkd__assembly_1__model_1

8wkd__assembly_1__model_1 | I(q)

8wkd__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 water

7. Citations (1)