2jla

Crystal structure of E.coli MenD, 2-succinyl-5-enolpyruvyl-6-hydroxy- 3-cyclohexadiene-1-carboxylate synthase - SeMet protein

Method: X-RAY DIFFRACTION

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

2-SUCCINYL-5-ENOLPYRUVYL-6-HYDROXY-3-CYCLOHEXENE -1-CARBOXYLATE SYNTHASE

ESCHERICHIA COLI

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	THIAMINE DIPHOSPHATE × 2 MANGANESE (II) ION × 2 CHLORIDE ION × 7 water × 2	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 2	THIAMINE DIPHOSPHATE × 2 MANGANESE (II) ION × 3 CHLORIDE ION × 6 water × 2	Consistent with protein count
3	Protein homooligomer	Homooligomer	Protein 4	THIAMINE DIPHOSPHATE × 4 MANGANESE (II) ION × 5 CHLORIDE ION × 13 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	MEND_ECOLI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 3–558； UniProt 1–556 Author chain B； PDBConstruct 3–558； UniProt 1–556 Author chain C； PDBConstruct 3–558； UniProt 1–556 Author chain D； PDBConstruct 3–558； UniProt 1–556

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	2jla
Deposition date deposition_date	2008-09-05
Structure title title	Crystal structure of E.coli MenD, 2-succinyl-5-enolpyruvyl-6-hydroxy- 3-cyclohexadiene-1-carboxylate synthase - SeMet protein
Keywords keywords	MANGANESE, TRANSFERASE, THIAMINE DIPHOSPHATE COFACTOR, THIAMINE PYROPHOSPHATE, MENAQUINONE BIOSYNTHESIS; 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.

2jla__assembly_1__model_1

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

Download this curve (.dat)

2jla__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2jla__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	31.88 Å
Rg (electron density)	31.09 Å
Total Rg	31.56 Å
Atom count	8723
Residues	1096
Excluded volume	154840 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2jla__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`2jla__assembly_2__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`2jla__assembly_3__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 (5)

Entity 1 Entity 1 polymer

Description description	2-SUCCINYL-5-ENOLPYRUVYL-6-HYDROXY-3-CYCLOHEXENE -1-CARBOXYLATE SYNTHASE
Molecular weight formula_weight	62004.2 kDa
EC 编号 ec_number	2.2.1.9
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	17841

GHMSVSAFNRRWAAVILEALTRHGVRHICIAPGSRSTPLTLAAAENSAFIHHTHFDERGLGHLALGLAKVSKQPVAVIVTSGTAVANLYPALIEAGLTGEKLILLTADRPPELIDCGANQAIRQPGMFASHPTHSISLPRPTQDIPARWLVSTIDHALGTLHAGGVHINCPFAEPLYGEMDDTGLSWQQRLGDWWQDDKPWLREAPRLESEKQRDWFFWRQKRGVVVAGRMSAEEGKKVALWAQTLGWPLIGDVLSQTGQPLPCADLWLGNAKATSELQQAQIVVQLGSSLTGKRLLQWQASCEPEEYWIVDDIEGRLDPAHHRGRRLIANIADWLELHPAEKRQPWCVEIPRLAEQAMQAVIARRDAFGEAQLAHRICDYLPEQGQLFVGNSLVVRLIDALSQLPAGYPVYSNRGASGIDGLLSTAAGVQRASGKPTLAIVGDLSALYDLNALALLRQVSAPLVLIVVNNNGGQIFSLLPTPQSERERFYLMPQNVHFEHAAAMFELKYHRPQNWQELETAFADAWRTPTTTVIEMVVNDTDGAQTLQQLLAQVSHL

Source Source

Source organism organism	ESCHERICHIA COLI
NCBI taxonomy ID ncbi_taxonomy_id	83333
Host organism host_organism	ESCHERICHIA COLI

Entity 2 Entity 2 non-polymer

Description description	THIAMINE DIPHOSPHATE
Molecular weight formula_weight	425.3 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 3 Entity 3 non-polymer

Description description	MANGANESE (II) ION
Molecular weight formula_weight	54.9 kDa
Source method src_method	syn
Copy count entity_count	5

Entity 4 Entity 4 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	13

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	395

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6. Fold Classification (SCOP + CATH) 12 domains

CATH v4.4 (12 domains)

Domain ID domain_id	2jlaA01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	970 — Thiamin diphosphate (ThDP)-binding fold, Pyr/PP domains

Domain ID domain_id	2jlaA02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1220 — TPP-binding domain

Domain ID domain_id	2jlaA03
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	970 — Thiamin diphosphate (ThDP)-binding fold, Pyr/PP domains

Domain ID domain_id	2jlaB01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	970 — Thiamin diphosphate (ThDP)-binding fold, Pyr/PP domains

Domain ID domain_id	2jlaB02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1220 — TPP-binding domain

Domain ID domain_id	2jlaB03
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	970 — Thiamin diphosphate (ThDP)-binding fold, Pyr/PP domains

Domain ID domain_id	2jlaC01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	970 — Thiamin diphosphate (ThDP)-binding fold, Pyr/PP domains

Domain ID domain_id	2jlaC02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1220 — TPP-binding domain

Domain ID domain_id	2jlaC03
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	970 — Thiamin diphosphate (ThDP)-binding fold, Pyr/PP domains

Domain ID domain_id	2jlaD01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	970 — Thiamin diphosphate (ThDP)-binding fold, Pyr/PP domains

Domain ID domain_id	2jlaD02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1220 — TPP-binding domain

Domain ID domain_id	2jlaD03
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	970 — Thiamin diphosphate (ThDP)-binding fold, Pyr/PP domains

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Unit-cell length a length_a	95.830 Å
Unit-cell length b length_b	95.830 Å
Unit-cell length c length_c	463.170 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	24

Space group space_group	P 65
Space-group number int_tables_number	170
Crystal system crystal_system	—

Resolution resolution	2.810 Å
Low-resolution limit resolution_low	83.050 Å
R factor r_factor	0.1720
R_work r_work	0.1690
R_free r_free	0.2330

Crystal structure of E.coli MenD, 2-succinyl-5-enolpyruvyl-6-hydroxy- 3-cyclohexadiene-1-carboxylate synthase - SeMet protein

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

2-SUCCINYL-5-ENOLPYRUVYL-6-HYDROXY-3-CYCLOHEXENE -1-CARBOXYLATE 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

2jla__assembly_1__model_1

2jla__assembly_1__model_1 | I(q)

2jla__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 (5)

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 water

6. Fold Classification (SCOP + CATH) 12 domains

CATH v4.4 (12 domains)

7. Citations (1)

Crystal structure of E.coli MenD, 2-succinyl-5-enolpyruvyl-6-hydroxy- 3-cyclohexadiene-1-carboxylate synthase - SeMet protein

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

2-SUCCINYL-5-ENOLPYRUVYL-6-HYDROXY-3-CYCLOHEXENE -1-CARBOXYLATE 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

2jla__assembly_1__model_1

2jla__assembly_1__model_1 | I(q)

2jla__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 (5)

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 water

6. Fold Classification (SCOP + CATH) 12 domains

CATH v4.4 (12 domains)

7. Citations (1)