2byo

Crystal structure of Mycobacterium tuberculosis lipoprotein LppX (Rv2945c)

Method: X-RAY DIFFRACTION

▼

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

LIPOPROTEIN LPPX

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	ZINC ION × 6 ACETATE ION × 1 DOCOSA-4,7,10,13,16,19-HEXAENOIC ACID × 1 ALPHA-LINOLENIC ACID × 2 OXALOACETATE ION × 1 D-MALATE × 1 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	LPPX_MYCTU
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–207； UniProt 27–233

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	2byo
Deposition date deposition_date	2005-08-03
Structure title title	Crystal structure of Mycobacterium tuberculosis lipoprotein LppX (Rv2945c)
Keywords keywords	LIPOPROTEIN, LIPID TRANSPORT, PALMITATE; LIPOPROTEIN
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.

2byo__assembly_1__model_1

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

Download this curve (.dat)

2byo__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2byo__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	17.95 Å
Rg (electron density)	16.41 Å
Total Rg	17.50 Å
Atom count	1438
Residues	183
Excluded volume	25844 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2byo__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download

▶

4. Crystallography and Experiment 4. Crystallography & Experiment

▶

5. Entities and Polymers Entities & Polymers (8)

Entity 1 Entity 1 polymer

Description description	LIPOPROTEIN LPPX
Molecular weight formula_weight	21532.0 kDa
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	1565

CSSPKPDAEEQGVPVSPTASDPALLAEIRQSLDATKGLTSVHVAVRTTGKVDSLLGITSADVDVRANPLAAKGVCTYNDEQGVPFRVQGDNISVKLFDDWSNLGSISELSTSRVLDPAAGVTQLLSGVTNLQAQGTEVIDGISTTKITGTIPASSVKMLDPGAKSARPATVWIAQDGSHHLVRASIDLGSGSIQLTQSKWNEPVNVD

Source Source

Source organism organism	MYCOBACTERIUM TUBERCULOSIS
NCBI taxonomy ID ncbi_taxonomy_id	83332
Host organism host_organism	ESCHERICHIA COLI

Entity 2 Entity 2 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 3 Entity 3 non-polymer

Description description	ACETATE ION
Molecular weight formula_weight	59.0 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	DOCOSA-4,7,10,13,16,19-HEXAENOIC ACID
Molecular weight formula_weight	328.5 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 non-polymer

Description description	ALPHA-LINOLENIC ACID
Molecular weight formula_weight	278.4 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 6 Entity 6 non-polymer

Description description	OXALOACETATE ION
Molecular weight formula_weight	131.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 7 Entity 7 non-polymer

Description description	D-MALATE
Molecular weight formula_weight	134.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 8 Entity 8 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	127

▼

6. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d2byoa1
Class class	b — All beta proteins
Fold Fold fold	b.125 — LolA-like prokaryotic lipoproteins and lipoprotein localization factors
Superfamily Superfamily superfamily	b.125.1 — Prokaryotic lipoproteins and lipoprotein localization factors
Family Family family	b.125.1.3 — LppX-like

CATH v4.4 (1 domains)

Domain ID domain_id	2byoA00
Class class	2 — Mainly Beta
Architecture architecture	50 — Clam
Topology topology	20 — outer membrane lipoprotein receptor (LolB), chain A
Homologous superfamily homologous superfamily	20 —

▶

Unit-cell length a length_a	54.257 Å
Unit-cell length b length_b	54.257 Å
Unit-cell length c length_c	269.983 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	12

Space group space_group	P 65 2 2
Space-group number int_tables_number	179
Crystal system crystal_system	—

Resolution resolution	2.150 Å
Low-resolution limit resolution_low	19.140 Å
R factor r_factor	0.1890
R_work r_work	0.1850
R_free r_free	0.2240

Crystal structure of Mycobacterium tuberculosis lipoprotein LppX (Rv2945c)

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

LIPOPROTEIN LPPX

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

2byo__assembly_1__model_1

2byo__assembly_1__model_1 | I(q)

2byo__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 (8)

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 water

6. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

CATH v4.4 (1 domains)

7. Citations (1)

Crystal structure of Mycobacterium tuberculosis lipoprotein LppX (Rv2945c)

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

LIPOPROTEIN LPPX

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

2byo__assembly_1__model_1

2byo__assembly_1__model_1 | I(q)

2byo__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 (8)

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 water

6. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

CATH v4.4 (1 domains)

7. Citations (1)