SAXSdb — 2bh7

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

N-ACETYLMURAMOYL-L-ALANINE AMIDASE

OrganismNot specified

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 SULFATE ION × 12 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	YBJR_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	2bh7
Deposition date deposition_date	2005-01-07
Structure title title	Crystal structure of a SeMet derivative of AmiD at 2.2 angstroms
Keywords keywords	ZINC AMIDASE, PGRP, T7 LYSOZYME, AMPD, 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.

2bh7__assembly_1__model_1

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

Download this curve (.dat)

2bh7__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2bh7__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	26.61 Å
Rg (electron density)	25.85 Å
Total Rg	26.56 Å
Atom count	4120
Residues	502
Excluded volume	72759 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2bh7__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 (4)

Entity 1 Entity 1 polymer

Description description	N-ACETYLMURAMOYL-L-ALANINE AMIDASE
Molecular weight formula_weight	29563.8 kDa
EC 编号 ec_number	3.5.1.28
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	2207

MGAGEKGIVEKEGYQLDTRRQAQAAYPRIKVLVIHYTADDFDSSLATLTDKQVSSHYLVPAVPPRYNGKPRIWQLVPEQELAWHAGISAWRGATRLNDTSIGIELENRGWQKSAGVKYFAPFEPAQIQALIPLAKDIIARYHIKPENVVAHADIAPQRKDDPGPLFPWQQLAQQGIGAWPDAQRVNFYLAGRAPHTPVDTASLLELLARYGYDVKPDMTPREQRRVIMAFQMHFRPTLYNGEADAETQAIAEALLEKYGQD

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

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	147

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6. Fold Classification (SCOP + CATH) 5 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d2bh7a1
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	d2bh7a2
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	2bh7A01
Class class	6 — Special
Architecture architecture	20 — Other non-globular
Topology topology	370 — Rhinovirus 14, subunit 4
Homologous superfamily homologous superfamily	150 —

Domain ID domain_id	2bh7A02
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	2bh7A03
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	2.200 Å
Low-resolution limit resolution_low	27.770 Å
R factor r_factor	0.2310
R_work r_work	0.2310
R_free r_free	0.2790

Crystal structure of a SeMet derivative of AmiD at 2.2 angstroms

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

N-ACETYLMURAMOYL-L-ALANINE AMIDASE

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

2bh7__assembly_1__model_1

2bh7__assembly_1__model_1 | I(q)

2bh7__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 (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 5 domains

SCOP 2.08 (2 domains)

CATH v4.4 (3 domains)

7. Citations (1)

Crystal structure of a SeMet derivative of AmiD at 2.2 angstroms

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

N-ACETYLMURAMOYL-L-ALANINE AMIDASE

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

2bh7__assembly_1__model_1

2bh7__assembly_1__model_1 | I(q)

2bh7__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 (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 5 domains

SCOP 2.08 (2 domains)

CATH v4.4 (3 domains)

7. Citations (1)