SAXSdb — 2y28

▼

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

1,6-ANHYDRO-N-ACETYLMURAMYL-L-ALANINE AMIDASE AMPD

CITROBACTER FREUNDII

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	ZINC ION × 1 water × 1	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	ZINC ION × 1 water × 1	Consistent with protein count
3	Protein monomer	Monomer	Protein 1	ZINC ION × 1 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	AMPD_CITFR
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–187； UniProt 1–187 Author chain B； PDBConstruct 1–187； UniProt 1–187 Author chain C； PDBConstruct 1–187； UniProt 1–187

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	2y28
Deposition date deposition_date	2010-12-14
Structure title title	crystal structure of Se-Met AmpD derivative
Keywords keywords	HYDROLASE, PEPTIDOGLYCAN AMIDASE, AMIDASE_2 FAMILY, ACTIVATION MECHANISM; HYDROLASE
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.

2y28__assembly_3__model_1

Assembly 3 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

2y28__assembly_3__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2y28__assembly_3__model_1 | P(r) · Pending

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

Rg（Guinier）	16.31 Å
Rg (electron density)	15.06 Å
Total Rg	16.09 Å
Atom count	1409
Residues	177
Excluded volume	24745 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2y28__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`2y28__assembly_2__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`2y28__assembly_3__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download

▶

4. Crystallography and Experiment 4. Crystallography & Experiment

▶

5. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	1,6-ANHYDRO-N-ACETYLMURAMYL-L-ALANINE AMIDASE AMPD
Molecular weight formula_weight	21012.0 kDa
EC 编号 ec_number	3.5.1.28
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C
Atom count atom_count	4921

MLLDEGWLAEARRVPSPHYDCRPDDENPSLLVVHNISLPPGEFGGPWIDALFTGTIDPNAHPYFAGIAHLRVSAHCLIRRDGEIVQYVPFDKRAWHAGVSSYQGRERCNDFSIGIELEGTDTLAYTDAQYQQLAAVTNALITRYPAIANNMTGHCNIAPERKTDPGPSFDWARFRALVTPSSHKEMT

Source Source

Source organism organism	CITROBACTER FREUNDII
NCBI taxonomy ID ncbi_taxonomy_id	546
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	3

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	689

▼

6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (3 domains)

Domain ID domain_id	d2y28a_
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

Domain ID domain_id	d2y28b_
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

Domain ID domain_id	d2y28c_
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 (3 domains)

Domain ID domain_id	2y28A00
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	2y28B00
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	2y28C00
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

▶

Unit-cell length a length_a	67.693 Å
Unit-cell length b length_b	67.693 Å
Unit-cell length c length_c	92.681 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	9

Space group space_group	P 32
Space-group number int_tables_number	145
Crystal system crystal_system	—

Resolution resolution	1.800 Å
Low-resolution limit resolution_low	58.624 Å
R factor r_factor	0.1835
R_work r_work	0.1780
R_free r_free	0.2318

crystal structure of Se-Met AmpD derivative

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

1,6-ANHYDRO-N-ACETYLMURAMYL-L-ALANINE AMIDASE AMPD

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

2y28__assembly_3__model_1

2y28__assembly_3__model_1 | I(q)

2y28__assembly_3__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (3 domains)

CATH v4.4 (3 domains)

7. Citations (1)

crystal structure of Se-Met AmpD derivative

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

1,6-ANHYDRO-N-ACETYLMURAMYL-L-ALANINE AMIDASE AMPD

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

2y28__assembly_3__model_1

2y28__assembly_3__model_1 | I(q)

2y28__assembly_3__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (3 domains)

CATH v4.4 (3 domains)

7. Citations (1)