SAXSdb — 2wkx

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

N-ACETYLMURAMOYL-L-ALANINE AMIDASE AMID

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	ZINC ION × 2 CHLORIDE ION × 4 GLYCEROL × 8 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	AMID_ECOLI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 3–261； UniProt 18–276

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	2wkx
Deposition date deposition_date	2009-06-18
Structure title title	Crystal structure of the native E. coli zinc amidase AmiD
Keywords keywords	OUTER MEMBRANE, CELL WALL BIOGENESIS/DEGRADATION, CELL MEMBRANE, METAL-BINDING, HYDROLASE; HYDROLASE
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.

2wkx__assembly_1__model_1

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

Download this curve (.dat)

2wkx__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2wkx__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	26.83 Å
Rg (electron density)	25.99 Å
Total Rg	26.75 Å
Atom count	4166
Residues	514
Excluded volume	73927 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2wkx__assembly_1__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	N-ACETYLMURAMOYL-L-ALANINE AMIDASE AMID
Molecular weight formula_weight	29376.2 kDa
EC 编号 ec_number	3.5.1.28
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	2351

MGAGEKGIVEKEGYQLDTRRQAQAAYPRIKVLVIHYTADDFDSSLATLTDKQVSSHYLVPAVPPRYNGKPRIWQLVPEQELAWHAGISAWRGATRLNDTSIGIELENRGWQKSAGVKYFAPFEPAQIQALIPLAKDIIARYHIKPENVVAHADIAPQRKDDPGPLFPWQQLAQQGIGAWPDAQRVNFYLAGRAPHTPVDTASLLELLARYGYDVKPDMTPREQRRVIMAFQMHFRPTLYNGEADAETQAIAEALLEKYGQD

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	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	239

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6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d2wkxa1
Class class	a — All alpha proteins
Fold Fold fold	a.20 — PGBD-like
Superfamily Superfamily superfamily	a.20.1 — PGBD-like
Family Family family	a.20.1.1 — Peptidoglycan binding domain, PGBD

Domain ID domain_id	d2wkxa2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.118 — N-acetylmuramoyl-L-alanine amidase-like
Superfamily Superfamily superfamily	d.118.1 — N-acetylmuramoyl-L-alanine amidase-like
Family Family family	d.118.1.1 — N-acetylmuramoyl-L-alanine amidase-like

CATH v4.4 (2 domains)

Domain ID domain_id	2wkxA01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	80 — Lysozyme-like
Homologous superfamily homologous superfamily	10 — Peptidoglycan recognition protein-like

Domain ID domain_id	2wkxA02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	101 — Muramoyl-pentapeptide Carboxypeptidase; domain 1
Homologous superfamily homologous superfamily	10 — PGBD-like superfamily/PGBD

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Unit-cell length a length_a	88.990 Å
Unit-cell length b length_b	88.990 Å
Unit-cell length c length_c	183.923 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 61 2 2
Space-group number int_tables_number	178
Crystal system crystal_system	—

Resolution resolution	1.800 Å
Low-resolution limit resolution_low	21.230 Å
R factor r_factor	0.1630
R_work r_work	0.1608
R_free r_free	0.1837

Crystal structure of the native E. coli zinc amidase AmiD

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

N-ACETYLMURAMOYL-L-ALANINE AMIDASE AMID

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

2wkx__assembly_1__model_1

2wkx__assembly_1__model_1 | I(q)

2wkx__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) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)

Crystal structure of the native E. coli zinc amidase AmiD

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

N-ACETYLMURAMOYL-L-ALANINE AMIDASE AMID

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

2wkx__assembly_1__model_1

2wkx__assembly_1__model_1 | I(q)

2wkx__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) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)