2dgk

Crystal structure of an N-terminal deletion mutant of Escherichia coli GadB in an autoinhibited state (aldamine)

Method: X-RAY DIFFRACTION

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

Glutamate decarboxylase beta

Escherichia coli

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 6	SULFATE ION × 6 PYRIDOXAL-5'-PHOSPHATE × 6 1,2-ETHANEDIOL × 8 water × 6	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 2	SULFATE ION × 2 PYRIDOXAL-5'-PHOSPHATE × 2 1,2-ETHANEDIOL × 3 water × 2	Consistent with protein count
3	Protein homooligomer	Homooligomer	Protein 2	SULFATE ION × 2 PYRIDOXAL-5'-PHOSPHATE × 2 1,2-ETHANEDIOL × 3 water × 2	Consistent with protein count
4	Protein homooligomer	Homooligomer	Protein 2	SULFATE ION × 2 PYRIDOXAL-5'-PHOSPHATE × 2 1,2-ETHANEDIOL × 2 water × 2	Consistent with protein count
5	Protein homooligomer	Homooligomer	Protein 2	SULFATE ION × 2 PYRIDOXAL-5'-PHOSPHATE × 2 1,2-ETHANEDIOL × 2 water × 2	Consistent with protein count
6	Protein homooligomer	Homooligomer	Protein 2	SULFATE ION × 2 PYRIDOXAL-5'-PHOSPHATE × 2 1,2-ETHANEDIOL × 2 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	DCEB_ECOLI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–452； UniProt 15–466 Author chain B； PDBConstruct 1–452； UniProt 15–466 Author chain C； PDBConstruct 1–452； UniProt 15–466 Author chain D； PDBConstruct 1–452； UniProt 15–466 Author chain E； PDBConstruct 1–452； UniProt 15–466 Author chain F； PDBConstruct 1–452； UniProt 15–466

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	2dgk
Deposition date deposition_date	2006-03-14
Structure title title	Crystal structure of an N-terminal deletion mutant of Escherichia coli GadB in an autoinhibited state (aldamine)
Keywords keywords	GadB, GadBD1-14, autoinhibition, substituted aldamine, 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.

2dgk__assembly_2__model_1

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

Download this curve (.dat)

2dgk__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2dgk__assembly_2__model_1 | P(r) · Pending

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

Rg（Guinier）	28.72 Å
Rg (electron density)	27.92 Å
Total Rg	28.67 Å
Atom count	7022
Residues	875
Excluded volume	124600 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2dgk__assembly_1__model_1`	hexameric （6）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`2dgk__assembly_2__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`2dgk__assembly_3__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`2dgk__assembly_4__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
5	1	`2dgk__assembly_5__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
6	1	`2dgk__assembly_6__model_1`	dimeric （2）	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	Glutamate decarboxylase beta
Molecular weight formula_weight	51067.0 kDa
EC 编号 ec_number	4.1.1.15
Mutation mutation	deletion of 14 N-terminal residues
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	22818

DSRFGAKSISTIAESKRFPLHEMRDDVAFQIINDELYLDGNARQNLATFCQTWDDENVHKLMDLSINKNWIDKEEYPQSAAIDLRCVNMVADLWHAPAPKNGQAVGTNTIGSSEACMLGGMAMKWRWRKRMEAAGKPTDKPNLVCGPVQICWHKFARYWDVELREIPMRPGQLFMDPKRMIEACDENTIGVVPTFGVTYTGNYEFPQPLHDALDKFQADTGIDIDMHIDAASGGFLAPFVAPDIVWDFRLPRVKSISASGHKFGLAPLGCGWVIWRDEEALPQELVFNVDYLGGQIGTFAINFSRPAGQVIAQYYEFLRLGREGYTKVQNASYQVAAYLADEIAKLGPYEFICTGRPDEGIPAVCFKLKDGEDPGYTLYDLSERLRLRGWQVPAFTLGGEATDIVVMRIMCRRGFEMDFAELLLEDYKASLKYLSDHPKLQGIAQQNSFKHT

Source Source

Source organism organism	Escherichia coli
NCBI taxonomy ID ncbi_taxonomy_id	562
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 3 Entity 3 non-polymer

Description description	PYRIDOXAL-5'-PHOSPHATE
Molecular weight formula_weight	247.1 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 4 Entity 4 non-polymer

Description description	1,2-ETHANEDIOL
Molecular weight formula_weight	62.1 kDa
Source method src_method	syn
Copy count entity_count	8

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	1695

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6. Fold Classification (SCOP + CATH) 18 domains

SCOP 2.08 (6 domains)

Domain ID domain_id	d2dgka_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.67 — PLP-dependent transferase-like
Superfamily Superfamily superfamily	c.67.1 — PLP-dependent transferases
Family Family family	c.67.1.6 — Pyridoxal-dependent decarboxylase

Domain ID domain_id	d2dgkb_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.67 — PLP-dependent transferase-like
Superfamily Superfamily superfamily	c.67.1 — PLP-dependent transferases
Family Family family	c.67.1.6 — Pyridoxal-dependent decarboxylase

Domain ID domain_id	d2dgkc_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.67 — PLP-dependent transferase-like
Superfamily Superfamily superfamily	c.67.1 — PLP-dependent transferases
Family Family family	c.67.1.6 — Pyridoxal-dependent decarboxylase

Domain ID domain_id	d2dgkd_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.67 — PLP-dependent transferase-like
Superfamily Superfamily superfamily	c.67.1 — PLP-dependent transferases
Family Family family	c.67.1.6 — Pyridoxal-dependent decarboxylase

Domain ID domain_id	d2dgke_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.67 — PLP-dependent transferase-like
Superfamily Superfamily superfamily	c.67.1 — PLP-dependent transferases
Family Family family	c.67.1.6 — Pyridoxal-dependent decarboxylase

Domain ID domain_id	d2dgkf_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.67 — PLP-dependent transferase-like
Superfamily Superfamily superfamily	c.67.1 — PLP-dependent transferases
Family Family family	c.67.1.6 — Pyridoxal-dependent decarboxylase

CATH v4.4 (12 domains)

Domain ID domain_id	2dgkA01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	640 — Aspartate Aminotransferase; domain 2
Homologous superfamily homologous superfamily	10 — Type I PLP-dependent aspartate aminotransferase-like (Major domain)

Domain ID domain_id	2dgkA02
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	1150 — Aspartate Aminotransferase, domain 1
Homologous superfamily homologous superfamily	160 —

Domain ID domain_id	2dgkB01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	640 — Aspartate Aminotransferase; domain 2
Homologous superfamily homologous superfamily	10 — Type I PLP-dependent aspartate aminotransferase-like (Major domain)

Domain ID domain_id	2dgkB02
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	1150 — Aspartate Aminotransferase, domain 1
Homologous superfamily homologous superfamily	160 —

Domain ID domain_id	2dgkC01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	640 — Aspartate Aminotransferase; domain 2
Homologous superfamily homologous superfamily	10 — Type I PLP-dependent aspartate aminotransferase-like (Major domain)

Domain ID domain_id	2dgkC02
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	1150 — Aspartate Aminotransferase, domain 1
Homologous superfamily homologous superfamily	160 —

Domain ID domain_id	2dgkD01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	640 — Aspartate Aminotransferase; domain 2
Homologous superfamily homologous superfamily	10 — Type I PLP-dependent aspartate aminotransferase-like (Major domain)

Domain ID domain_id	2dgkD02
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	1150 — Aspartate Aminotransferase, domain 1
Homologous superfamily homologous superfamily	160 —

Domain ID domain_id	2dgkE01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	640 — Aspartate Aminotransferase; domain 2
Homologous superfamily homologous superfamily	10 — Type I PLP-dependent aspartate aminotransferase-like (Major domain)

Domain ID domain_id	2dgkE02
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	1150 — Aspartate Aminotransferase, domain 1
Homologous superfamily homologous superfamily	160 —

Domain ID domain_id	2dgkF01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	640 — Aspartate Aminotransferase; domain 2
Homologous superfamily homologous superfamily	10 — Type I PLP-dependent aspartate aminotransferase-like (Major domain)

Domain ID domain_id	2dgkF02
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	1150 — Aspartate Aminotransferase, domain 1
Homologous superfamily homologous superfamily	160 —

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Unit-cell length a length_a	92.770 Å
Unit-cell length b length_b	158.560 Å
Unit-cell length c length_c	201.420 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	24

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	1.900 Å
Low-resolution limit resolution_low	30.000 Å
R factor r_factor	—
R_work r_work	0.2180
R_free r_free	0.2460

Crystal structure of an N-terminal deletion mutant of Escherichia coli GadB in an autoinhibited state (aldamine)

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

Glutamate decarboxylase beta

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

2dgk__assembly_2__model_1

2dgk__assembly_2__model_1 | I(q)

2dgk__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 (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) 18 domains

SCOP 2.08 (6 domains)

CATH v4.4 (12 domains)

7. Citations (2)

Crystal structure of an N-terminal deletion mutant of Escherichia coli GadB in an autoinhibited state (aldamine)

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

Glutamate decarboxylase beta

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

2dgk__assembly_2__model_1

2dgk__assembly_2__model_1 | I(q)

2dgk__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 (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) 18 domains

SCOP 2.08 (6 domains)

CATH v4.4 (12 domains)

7. Citations (2)