9pcs

Crystal structure of Dihydrodipicolinate Synthase from Mycobacterium tuberculosis in complex with pyruvate

Method: X-RAY DIFFRACTION

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

4-hydroxy-tetrahydrodipicolinate synthase

Mycobacterium tuberculosis H37Rv

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 4	PYRUVIC ACID × 4 GLYCEROL × 7 MAGNESIUM ION × 9 1,2-ETHANEDIOL × 5 water × 4	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 4	PYRUVIC ACID × 4 GLYCEROL × 6 MAGNESIUM ION × 10 1,2-ETHANEDIOL × 1 CHLORIDE ION × 3 DI(HYDROXYETHYL)ETHER × 1 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	DAPA_MYCTU
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–300； UniProt 1–300 Author chain B； PDBConstruct 1–300； UniProt 1–300 Author chain C； PDBConstruct 1–300； UniProt 1–300 Author chain D； PDBConstruct 1–300； UniProt 1–300 Author chain E； PDBConstruct 1–300； UniProt 1–300 Author chain F； PDBConstruct 1–300； UniProt 1–300 Author chain G； PDBConstruct 1–300； UniProt 1–300 Author chain H； PDBConstruct 1–300； 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	9pcs
Deposition date deposition_date	2025-06-29
Last revision last_revision	2025-10-08
Structure title title	Crystal structure of Dihydrodipicolinate Synthase from Mycobacterium tuberculosis in complex with pyruvate
Keywords keywords	Complex, Substrate, LYASE; LYASE
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.

9pcs__assembly_2__model_1

Assembly 2 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

9pcs__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

9pcs__assembly_2__model_1 | P(r) · Pending

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

Rg（Guinier）	32.13 Å
Rg (electron density)	30.75 Å
Total Rg	31.50 Å
Atom count	8606
Residues	1180
Excluded volume	153370 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`9pcs__assembly_1__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`9pcs__assembly_2__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 (8)

Entity 1 Entity 1 polymer

Description description	4-hydroxy-tetrahydrodipicolinate synthase
Molecular weight formula_weight	30888.2 kDa
EC 编号 ec_number	4.3.3.7
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	20242

MTTVGFDVAARLGTLLTAMVTPFSGDGSLDTATAARLANHLVDQGCDGLVVSGTTGESPTTTDGEKIELLRAVLEAVGDRARVIAGAGTYDTAHSIRLAKACAAEGAHGLLVVTPYYSKPPQRGLQAHFTAVADATELPMLLYDIPGRSAVPIEPDTIRALASHPNIVGVKDAKADLHSGAQIMADTGLAYYSGDDALNLPWLAMGATGFISVIAHLAAGQLRELLSAFGSGDIATARKINIAVAPLCNAMSRLGGVTLSKAGLRLQGIDVGDPRLPQVAATPEQIDALAADMRAASVLR

Source Source

Source organism organism	Mycobacterium tuberculosis H37Rv
NCBI taxonomy ID ncbi_taxonomy_id	83332
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	PYRUVIC ACID
Molecular weight formula_weight	88.1 kDa
Source method src_method	syn
Copy count entity_count	8

Entity 3 Entity 3 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	13

Entity 4 Entity 4 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	19

Entity 5 Entity 5 non-polymer

Description description	1,2-ETHANEDIOL
Molecular weight formula_weight	62.1 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 6 Entity 6 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 7 Entity 7 non-polymer

Description description	DI(HYDROXYETHYL)ETHER
Molecular weight formula_weight	106.1 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	2747

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Unit-cell length a length_a	95.470 Å
Unit-cell length b length_b	87.016 Å
Unit-cell length c length_c	141.059 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	107.19 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	16

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	1.500 Å
Low-resolution limit resolution_low	47.860 Å
R factor r_factor	0.1511
R_work r_work	0.1510
R_free r_free	0.1685

Crystal structure of Dihydrodipicolinate Synthase from Mycobacterium tuberculosis in complex with pyruvate

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

4-hydroxy-tetrahydrodipicolinate synthase

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

9pcs__assembly_2__model_1

9pcs__assembly_2__model_1 | I(q)

9pcs__assembly_2__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

7. Citations (1)

Crystal structure of Dihydrodipicolinate Synthase from Mycobacterium tuberculosis in complex with pyruvate

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

4-hydroxy-tetrahydrodipicolinate synthase

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

9pcs__assembly_2__model_1

9pcs__assembly_2__model_1 | I(q)

9pcs__assembly_2__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

7. Citations (1)