SAXSdb — 4mky

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

DNA ligase-like protein Rv0938/MT0965

Mycobacterium tuberculosis

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Homooligomer	Protein 2 DNA 4	5'-D(PDGPDCPDGPDGPDC)-3' × 2 5'-D(DGPDCPDCPDGPDCPDAPDGPDTPDAP*DC)-3' × 2 water × 5	Consistent with all polymers
2	Protein–DNA	Homooligomer	Protein 2 DNA 4	5'-D(PDGPDCPDGPDGPDC)-3' × 2 5'-D(DGPDCPDCPDGPDCPDAPDGPDTPDAP*DC)-3' × 2 water × 5	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Y938_MYCTU
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 4–303； UniProt 1–300 Author chain B； PDBConstruct 4–303； UniProt 1–300 Author chain C； PDBConstruct 4–303； UniProt 1–300 Author chain D； PDBConstruct 4–303； UniProt 1–300

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	4mky
Deposition date deposition_date	2013-09-05
Structure title title	Polymerase Domain from Mycobacterium tuberculosis Ligase D in complex with an annealed double-strand DNA break.
Keywords keywords	protein-DNA complex, transferase-DNA complex, Nucleotide-binding, polymerase, primase, transferase; TRANSFERASE/DNA
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.

4mky__assembly_1__model_1

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

Download this curve (.dat)

4mky__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

4mky__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	27.61 Å
Rg (electron density)	26.94 Å
Total Rg	27.65 Å
Atom count	4866
Residues	593
Excluded volume	84725 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`4mky__assembly_1__model_1`	hexameric （6）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`4mky__assembly_2__model_1`	hexameric （6）	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	DNA ligase-like protein Rv0938/MT0965
Molecular weight formula_weight	32825.1 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	9936

GSHMGSASEQRVTLTNADKVLYPATGTTKSDIFDYYAGVAEVMLGHIAGRPATRKRWPNGVDQPAFFEKQLALSAPPWLSRATVAHRSGTTTYPIIDSATGLAWIAQQAALEVHVPQWRFVAEPGSGELNPGPATRLVFDLDPGEGVMMAQLAEVARAVRDLLADIGLVTFPVTSGSKGLHLYTPLDEPVSSRGATVLAKRVAQRLEQAMPALVTSTMTKSLRAGKVFVDWSQNSGSKTTIAPYSLRGRTHPTVAAPRTWAELDDPALRQLSYDEVLTRIARDGDLLERLDADAPVADRLTRY

Source Source

Source organism organism	Mycobacterium tuberculosis
NCBI taxonomy ID ncbi_taxonomy_id	1773
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	5'-D(PDGPDCPDGPDGP*DC)-3'
Molecular weight formula_weight	1521.0 kDa
Source method src_method	syn
Copy count entity_count	4

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	E,G,I,K

GCGGC

Entity 3 Entity 3 polymer

Description description	5'-D(DGPDCPDCPDGPDCPDAPDGPDTPDAPDC)-3'
Molecular weight formula_weight	3030.0 kDa
Source method src_method	syn
Copy count entity_count	4

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	F,H,J,L

GCCGCAGTAC

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	196

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6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id	4mkyA02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	3300 —

Domain ID domain_id	4mkyB02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	3300 —

Domain ID domain_id	4mkyC02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	3300 —

Domain ID domain_id	4mkyD02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	3300 —

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Unit-cell length a length_a	87.580 Å
Unit-cell length b length_b	80.110 Å
Unit-cell length c length_c	118.390 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	111.62 °
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	2.400 Å
Low-resolution limit resolution_low	37.640 Å
R factor r_factor	0.1997
R_work r_work	0.1973
R_free r_free	0.2453

Polymerase Domain from Mycobacterium tuberculosis Ligase D in complex with an annealed double-strand DNA break.

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

DNA ligase-like protein Rv0938/MT0965

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

4mky__assembly_1__model_1

4mky__assembly_1__model_1 | I(q)

4mky__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

Entity 3 Entity 3 polymer

Polymer Polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

7. Citations (1)

Polymerase Domain from Mycobacterium tuberculosis Ligase D in complex with an annealed double-strand DNA break.

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

DNA ligase-like protein Rv0938/MT0965

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

4mky__assembly_1__model_1

4mky__assembly_1__model_1 | I(q)

4mky__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

Entity 3 Entity 3 polymer

Polymer Polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

7. Citations (1)