SAXSdb — 9hty

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

N-acetylmuramoyl-L-alanine amidase

Mycobacterium phage DS6A

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 6	L-Ala-D-iso-Gln-L-Lys- D-Ala-D-Ala × 3 PHOSPHATE ION × 3 ZINC ION × 3 water × 5	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	G8I4E0_9CAUD
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 3–192； UniProt 206–395 Author chain B； PDBConstruct 3–192； UniProt 206–395 Author chain C； PDBConstruct 3–192； UniProt 206–395

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	9hty
Deposition date deposition_date	2024-12-20
Last revision last_revision	2026-04-22
Structure title title	Crystal structure of Ami2B domain of DS6A-LysA in complex with L-Ala-D-iso-Gln-L-Lys- D-Ala-D-Ala
Keywords keywords	Peptidoglycan hydrolase, Amidase, DS6A-LysA, crystal complex, 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.

9hty__assembly_1__model_1

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

Download this curve (.dat)

9hty__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

9hty__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	25.84 Å
Rg (electron density)	25.14 Å
Total Rg	25.86 Å
Atom count	4446
Residues	570
Excluded volume	78021 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`9hty__assembly_1__model_1`	hexameric （6）	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
Molecular weight formula_weight	21246.1 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	4515

GPGMAWTGDPVWLEDVLRPVLGDRLRVLPSWQMYGHGDFKDIRGVMVHHTGNARETAESIRKGRPDLRGPLSNIHIAPDGTVTLVAAGVCWHAGAGSYPWLPTNNANWHMIGIECAWPTIRPNGTYDEREPWPDAQIIAMRDTCAALTKRLGWDASRVIGHKEYAGASQGKWDPGNLDMGWFRGEVAKAMRG

Source Source

Source organism organism	Mycobacterium phage DS6A
NCBI taxonomy ID ncbi_taxonomy_id	45764
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 polymer

Description description	L-Ala-D-iso-Gln-L-Lys- D-Ala-D-Ala
Molecular weight formula_weight	488.6 kDa
Source method src_method	syn
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	F,H,I

AXKAA

Entity 3 Entity 3 non-polymer

Description description	PHOSPHATE ION
Molecular weight formula_weight	95.0 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 4 Entity 4 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	nat
Copy count entity_count	3

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	69

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Unit-cell length a length_a	70.683 Å
Unit-cell length b length_b	121.237 Å
Unit-cell length c length_c	80.052 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	106.25 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	12

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	monoclinic

Resolution resolution	2.740 Å
Low-resolution limit resolution_low	60.620 Å
R factor r_factor	0.1639
R_work r_work	0.1622
R_free r_free	0.1970

Crystal structure of Ami2B domain of DS6A-LysA in complex with L-Ala-D-iso-Gln-L-Lys- D-Ala-D-Ala

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

9hty__assembly_1__model_1

9hty__assembly_1__model_1 | I(q)

9hty__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 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

7. Citations (1)

Crystal structure of Ami2B domain of DS6A-LysA in complex with L-Ala-D-iso-Gln-L-Lys- D-Ala-D-Ala

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

9hty__assembly_1__model_1

9hty__assembly_1__model_1 | I(q)

9hty__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 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

7. Citations (1)