3nue

The structure of 3-deoxy-d-arabino-heptulosonate 7-phosphate synthase from mycobacterium tuberculosis complexed with tryptophan

Method: X-RAY DIFFRACTION

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

Probable 3-deoxy-D-arabino-heptulosonate 7-phosphate synthase AroG

Mycobacterium tuberculosis

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 4	MANGANESE (II) ION × 4 TRYPTOPHAN × 4 PHOSPHATE ION × 4 SULFATE ION × 8 GLYCEROL × 14 O-DODECANYL OCTAETHYLENE GLYCOL × 2 CHLORIDE ION × 2 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	O53512_MYCTU
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 3–464； UniProt 1–462 Author chain B； PDBConstruct 3–464； UniProt 1–462

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	3nue
Deposition date deposition_date	2010-07-06
Structure title title	The structure of 3-deoxy-d-arabino-heptulosonate 7-phosphate synthase from mycobacterium tuberculosis complexed with tryptophan
Keywords keywords	;Mycobacterium tuberculosis, DAH7P synthase, Shikimate pathway, Aromatic biosynthesis, Evolutionary relationships, Transferase, TRP-bound, Augmented TIM-barrel structure ;; 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.

3nue__assembly_1__model_1

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

Download this curve (.dat)

3nue__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3nue__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	39.67 Å
Rg (electron density)	38.90 Å
Total Rg	39.35 Å
Atom count	13984
Residues	1792
Excluded volume	247280 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3nue__assembly_1__model_1`	tetrameric （4）	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	Probable 3-deoxy-D-arabino-heptulosonate 7-phosphate synthase AroG
Molecular weight formula_weight	50828.4 kDa
EC 编号 ec_number	2.5.1.54
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	7431

GAMNWTVDIPIDQLPSLPPLPTDLRTRLDAALAKPAAQQPTWPADQALAMRTVLESVPPVTVPSEIVRLQEQLAQVAKGEAFLLQGGDCAETFMDNTEPHIRGNVRALLQMAVVLTYGASMPVVKVARIAGQYAKPRSADIDALGLRSYRGDMINGFAPDAAAREHDPSRLVRAYANASAAMNLVRALTSSGLASLHLVHDWNREFVRTSPAGARYEALATEIDRGLRFMSACGVADRNLQTAEIYASHEALVLDYERAMLRLSDGDDGEPQLFDLSAHTVWIGERTRQIDGAHIAFAQVIANPVGVKLGPNMTPELAVEYVERLDPHNKPGRLTLVSRMGNHKVRDLLPPIVEKVQATGHQVIWQCDPMHGNTHESSTGFKTRHFDRIVDEVQGFFEVHRALGTHPGGIHVEITGENVTECLGGAQDISETDLAGRYETACDPRLNTQQSLELAFLVAEMLRD

Source Source

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

Entity 2 Entity 2 non-polymer

Description description	MANGANESE (II) ION
Molecular weight formula_weight	54.9 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 non-polymer

Description description	TRYPTOPHAN
Molecular weight formula_weight	204.2 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 non-polymer

Description description	PHOSPHATE ION
Molecular weight formula_weight	95.0 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 6 Entity 6 non-polymer

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

Entity 7 Entity 7 non-polymer

Description description	O-DODECANYL OCTAETHYLENE GLYCOL
Molecular weight formula_weight	538.8 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 8 Entity 8 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 9 Entity 9 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	297

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6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d3nuea1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamily	c.1.10 — Aldolase
Family Family family	c.1.10.8 — Class-II DAHP synthetase

Domain ID domain_id	d3nuea2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d3nueb1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamily	c.1.10 — Aldolase
Family Family family	c.1.10.8 — Class-II DAHP synthetase

Domain ID domain_id	d3nueb2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

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Unit-cell length a length_a	204.712 Å
Unit-cell length b length_b	204.712 Å
Unit-cell length c length_c	66.264 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 32 2 1
Space-group number int_tables_number	154
Crystal system crystal_system	—

Resolution resolution	2.500 Å
Low-resolution limit resolution_low	38.690 Å
R factor r_factor	0.1910
R_work r_work	0.1890
R_free r_free	0.2281

The structure of 3-deoxy-d-arabino-heptulosonate 7-phosphate synthase from mycobacterium tuberculosis complexed with tryptophan

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

Probable 3-deoxy-D-arabino-heptulosonate 7-phosphate synthase AroG

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

3nue__assembly_1__model_1

3nue__assembly_1__model_1 | I(q)

3nue__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 (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

SCOP 2.08 (4 domains)

7. Citations (1)

The structure of 3-deoxy-d-arabino-heptulosonate 7-phosphate synthase from mycobacterium tuberculosis complexed with tryptophan

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

Probable 3-deoxy-D-arabino-heptulosonate 7-phosphate synthase AroG

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

3nue__assembly_1__model_1

3nue__assembly_1__model_1 | I(q)

3nue__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 (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

SCOP 2.08 (4 domains)

7. Citations (1)