7kpc

Dihydrodipicolinate synthase (DHDPS) from C.jejuni, E88Q mutant with pyruvate bound in the active site and L-lysine bound at the allosteric site

Method: X-RAY DIFFRACTION

▼

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

4-hydroxy-tetrahydrodipicolinate synthase

Campylobacter jejuni subsp. jejuni serotype O:2 (strain ATCC 700819 / NCTC 11168)

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	LYSINE × 2 MAGNESIUM ION × 7 ACETATE ION × 6 1,2-ETHANEDIOL × 11 TRIETHYLENE GLYCOL × 5 DI(HYDROXYETHYL)ETHER × 2 GLYCEROL × 1 water × 2	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 2	LYSINE × 2 MAGNESIUM ION × 4 ACETATE ION × 4 1,2-ETHANEDIOL × 8 TRIETHYLENE GLYCOL × 3 DI(HYDROXYETHYL)ETHER × 7 GLYCEROL × 1 water × 2	Consistent with protein count
3	Protein homooligomer	Homooligomer	Protein 2	LYSINE × 2 MAGNESIUM ION × 3 ACETATE ION × 5 1,2-ETHANEDIOL × 9 TRIETHYLENE GLYCOL × 2 DI(HYDROXYETHYL)ETHER × 3 GLYCEROL × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	DAPA_CAMJE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 13–310； UniProt 1–298 Author chain B； PDBConstruct 13–310； UniProt 1–298 Author chain C； PDBConstruct 13–310； UniProt 1–298 Author chain D； PDBConstruct 13–310； UniProt 1–298 Author chain E； PDBConstruct 13–310； UniProt 1–298 Author chain F； PDBConstruct 13–310； UniProt 1–298

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	7kpc
Deposition date deposition_date	2020-11-10
Structure title title	Dihydrodipicolinate synthase (DHDPS) from C.jejuni, E88Q mutant with pyruvate bound in the active site and L-lysine bound at the allosteric site
Keywords keywords	Dihydrodipicolinate synthase, LYASE; LYASE
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.

7kpc__assembly_1__model_1

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

Download this curve (.dat)

7kpc__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

7kpc__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	25.66 Å
Rg (electron density)	24.77 Å
Total Rg	25.63 Å
Atom count	4668
Residues	589
Excluded volume	84070 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`7kpc__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`7kpc__assembly_2__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`7kpc__assembly_3__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download

▶

4. Crystallography and Experiment 4. Crystallography & Experiment

▶

5. Entities and Polymers Entities & Polymers (9)

Entity 1 Entity 1 polymer

Description description	4-hydroxy-tetrahydrodipicolinate synthase
Molecular weight formula_weight	34184.3 kDa
EC 编号 ec_number	4.3.3.7
Mutation mutation	E88Q
Source method src_method	man
Copy count entity_count	6

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F
Atom count atom_count	15646

MRGSHHHHHHGSMDKNIIIGAMTALITPFKNGKVDEQSYARLIKRQIENGIDAVVPVGTTGESATLTHEEHRTCIEIAVETCKGTKVKVLAGAGSNATHQAVGLAKFAKEHGADGILSVAPYYNKPTQQGLYEHYKAIAQSVDIPVLLYNVPGRTGCEISTDTIIKLFRDCENIYGVKEASGNIDKCVDLLAHEPRMMLISGEDAINYPILSNGGKGVISVTSNLLPDMISALTHFALDENYKEAKKINDELYNINKILFCESNPIPIKTAMYLAGLIESLEFRLPLCSPSKENFAKIEEVMKKYKIKGF

Source Source

Source organism organism	Campylobacter jejuni subsp. jejuni serotype O:2 (strain ATCC 700819 / NCTC 11168)
NCBI taxonomy ID ncbi_taxonomy_id	192222
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	LYSINE
Molecular weight formula_weight	147.2 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 3 Entity 3 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	14

Entity 4 Entity 4 non-polymer

Description description	ACETATE ION
Molecular weight formula_weight	59.0 kDa
Source method src_method	syn
Copy count entity_count	15

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	28

Entity 6 Entity 6 non-polymer

Description description	TRIETHYLENE GLYCOL
Molecular weight formula_weight	150.2 kDa
Source method src_method	nat
Copy count entity_count	10

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	12

Entity 8 Entity 8 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 9 Entity 9 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	1539

▶

Unit-cell length a length_a	85.350 Å
Unit-cell length b length_b	231.610 Å
Unit-cell length c length_c	199.850 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	48

Space group space_group	C 2 2 21
Space-group number int_tables_number	20
Crystal system crystal_system	—

Resolution resolution	1.760 Å
Low-resolution limit resolution_low	43.700 Å
R factor r_factor	0.1431
R_work r_work	0.1418
R_free r_free	0.1686

Dihydrodipicolinate synthase (DHDPS) from C.jejuni, E88Q mutant with pyruvate bound in the active site and L-lysine bound at the allosteric site

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

7kpc__assembly_1__model_1

7kpc__assembly_1__model_1 | I(q)

7kpc__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

7. Citations (1)

Dihydrodipicolinate synthase (DHDPS) from C.jejuni, E88Q mutant with pyruvate bound in the active site and L-lysine bound at the allosteric site

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

7kpc__assembly_1__model_1

7kpc__assembly_1__model_1 | I(q)

7kpc__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

7. Citations (1)