1yk3

Crystal structure of Rv1347c from Mycobacterium tuberculosis

Method: X-RAY DIFFRACTION

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

Hypothetical protein Rv1347c/MT1389

Mycobacterium tuberculosis

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	water × 1	Consistent with protein count
10	Protein homooligomer	Homooligomer	Protein 2	octyl beta-D-glucopyranoside × 1 water × 2	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	water × 1	Consistent with protein count
3	Protein monomer	Monomer	Protein 1	water × 1	Consistent with protein count
4	Protein monomer	Monomer	Protein 1	octyl beta-D-glucopyranoside × 1 water × 1	Consistent with protein count
5	Protein monomer	Monomer	Protein 1	octyl beta-D-glucopyranoside × 1 water × 1	Consistent with protein count
6	Protein monomer	Monomer	Protein 1	water × 1	Consistent with protein count
7	Protein monomer	Monomer	Protein 1	octyl beta-D-glucopyranoside × 1 water × 1	Consistent with protein count
8	Protein monomer	Monomer	Protein 1	water × 1	Consistent with protein count
9	Protein homooligomer	Homooligomer	Protein 2	water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Y1347_MYCTU
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–210； UniProt 1–210 Author chain B； PDBConstruct 1–210； UniProt 1–210 Author chain C； PDBConstruct 1–210； UniProt 1–210 Author chain D； PDBConstruct 1–210； UniProt 1–210 Author chain E； PDBConstruct 1–210； UniProt 1–210 Author chain F； PDBConstruct 1–210； UniProt 1–210 Author chain G； PDBConstruct 1–210； UniProt 1–210 Author chain H； PDBConstruct 1–210； UniProt 1–210

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	1yk3
Deposition date deposition_date	2005-01-16
Structure title title	Crystal structure of Rv1347c from Mycobacterium tuberculosis
Keywords keywords	;acyltransferase, GCN5-related fold, Structural Genomics, PSI, Protein Structure Initiative, TB Structural Genomics Consortium, TBSGC, TRANSFERASE ;; TRANSFERASE
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.

1yk3__assembly_1__model_1

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

Download this curve (.dat)

1yk3__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1yk3__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	17.51 Å
Rg (electron density)	16.14 Å
Total Rg	17.18 Å
Atom count	1600
Residues	198
Excluded volume	28175 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1yk3__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`1yk3__assembly_2__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`1yk3__assembly_3__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`1yk3__assembly_4__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
5	1	`1yk3__assembly_5__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
6	1	`1yk3__assembly_6__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
7	1	`1yk3__assembly_7__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
8	1	`1yk3__assembly_8__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
9	1	`1yk3__assembly_9__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
10	1	`1yk3__assembly_10__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 (3)

Entity 1 Entity 1 polymer

Description description	Hypothetical protein Rv1347c/MT1389
Molecular weight formula_weight	23830.0 kDa
Source method src_method	man
Copy count entity_count	8

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F,G,H
Atom count atom_count	13515

MTKPTSAGQADDALVRLARERFDLPDQVRRLARPPVPSLEPPYGLRVAQLTDAEMLAEWMNRPHLAAAWEYDWPASRWRQHLNAQLEGTYSLPLIGSWHGTDGGYLELYWAAKDLISHYYDADPYDLGLHAAIADLSKVNRGFGPLLLPRIVASVFANEPRCRRIMFDPDHRNTATRRLCEWAGCKFLGEHDTTNRRMALYALEAPTTAA

Source Source

Source organism organism	Mycobacterium tuberculosis
NCBI taxonomy ID ncbi_taxonomy_id	1773
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 non-polymer

Description description	octyl beta-D-glucopyranoside
Molecular weight formula_weight	292.4 kDa
Source method src_method	man
Copy count entity_count	3

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	650

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6. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

Domain ID domain_id	d1yk3a1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.108 — Acyl-CoA N-acyltransferases (Nat)
Superfamily Superfamily superfamily	d.108.1 — Acyl-CoA N-acyltransferases (Nat)
Family Family family	d.108.1.1 — N-acetyl transferase, NAT

Domain ID domain_id	d1yk3b_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.108 — Acyl-CoA N-acyltransferases (Nat)
Superfamily Superfamily superfamily	d.108.1 — Acyl-CoA N-acyltransferases (Nat)
Family Family family	d.108.1.1 — N-acetyl transferase, NAT

Domain ID domain_id	d1yk3c_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.108 — Acyl-CoA N-acyltransferases (Nat)
Superfamily Superfamily superfamily	d.108.1 — Acyl-CoA N-acyltransferases (Nat)
Family Family family	d.108.1.1 — N-acetyl transferase, NAT

Domain ID domain_id	d1yk3d_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.108 — Acyl-CoA N-acyltransferases (Nat)
Superfamily Superfamily superfamily	d.108.1 — Acyl-CoA N-acyltransferases (Nat)
Family Family family	d.108.1.1 — N-acetyl transferase, NAT

Domain ID domain_id	d1yk3e_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.108 — Acyl-CoA N-acyltransferases (Nat)
Superfamily Superfamily superfamily	d.108.1 — Acyl-CoA N-acyltransferases (Nat)
Family Family family	d.108.1.1 — N-acetyl transferase, NAT

Domain ID domain_id	d1yk3f_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.108 — Acyl-CoA N-acyltransferases (Nat)
Superfamily Superfamily superfamily	d.108.1 — Acyl-CoA N-acyltransferases (Nat)
Family Family family	d.108.1.1 — N-acetyl transferase, NAT

Domain ID domain_id	d1yk3g_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.108 — Acyl-CoA N-acyltransferases (Nat)
Superfamily Superfamily superfamily	d.108.1 — Acyl-CoA N-acyltransferases (Nat)
Family Family family	d.108.1.1 — N-acetyl transferase, NAT

Domain ID domain_id	d1yk3h_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.108 — Acyl-CoA N-acyltransferases (Nat)
Superfamily Superfamily superfamily	d.108.1 — Acyl-CoA N-acyltransferases (Nat)
Family Family family	d.108.1.1 — N-acetyl transferase, NAT

CATH v4.4 (8 domains)

Domain ID domain_id	1yk3A00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	630 — Aminopeptidase
Homologous superfamily homologous superfamily	30 — Gcn5-related N-acetyltransferase (GNAT)

Domain ID domain_id	1yk3B00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	630 — Aminopeptidase
Homologous superfamily homologous superfamily	30 — Gcn5-related N-acetyltransferase (GNAT)

Domain ID domain_id	1yk3C00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	630 — Aminopeptidase
Homologous superfamily homologous superfamily	30 — Gcn5-related N-acetyltransferase (GNAT)

Domain ID domain_id	1yk3D00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	630 — Aminopeptidase
Homologous superfamily homologous superfamily	30 — Gcn5-related N-acetyltransferase (GNAT)

Domain ID domain_id	1yk3E00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	630 — Aminopeptidase
Homologous superfamily homologous superfamily	30 — Gcn5-related N-acetyltransferase (GNAT)

Domain ID domain_id	1yk3F00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	630 — Aminopeptidase
Homologous superfamily homologous superfamily	30 — Gcn5-related N-acetyltransferase (GNAT)

Domain ID domain_id	1yk3G00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	630 — Aminopeptidase
Homologous superfamily homologous superfamily	30 — Gcn5-related N-acetyltransferase (GNAT)

Domain ID domain_id	1yk3H00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	630 — Aminopeptidase
Homologous superfamily homologous superfamily	30 — Gcn5-related N-acetyltransferase (GNAT)

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Unit-cell length a length_a	75.665 Å
Unit-cell length b length_b	77.261 Å
Unit-cell length c length_c	296.514 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	32

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

Resolution resolution	2.200 Å
Low-resolution limit resolution_low	36.960 Å
R factor r_factor	0.2270
R_work r_work	0.2270
R_free r_free	0.2580

Crystal structure of Rv1347c from Mycobacterium tuberculosis

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

Hypothetical protein Rv1347c/MT1389

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

1yk3__assembly_1__model_1

1yk3__assembly_1__model_1 | I(q)

1yk3__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

5. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

CATH v4.4 (8 domains)

7. Citations (1)

Crystal structure of Rv1347c from Mycobacterium tuberculosis

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

Hypothetical protein Rv1347c/MT1389

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

1yk3__assembly_1__model_1

1yk3__assembly_1__model_1 | I(q)

1yk3__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

5. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

CATH v4.4 (8 domains)

7. Citations (1)