SAXSdb — 1m22

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

peptide amidase

Stenotrophomonas maltophilia

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 1 water × 1	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 1 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q8RJN5_XANMA
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–503； UniProt 38–540 Author chain B； PDBConstruct 1–503； UniProt 38–540

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	1m22
Deposition date deposition_date	2002-06-21
Structure title title	X-ray structure of native peptide amidase from Stenotrophomonas maltophilia at 1.4 A
Keywords keywords	eleven-stranded beta sheet, covered double layers of alpha helices on top and bottom, 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.

1m22__assembly_1__model_1

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

Download this curve (.dat)

1m22__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1m22__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	22.47 Å
Rg (electron density)	21.24 Å
Total Rg	22.11 Å
Atom count	3664
Residues	487
Excluded volume	64836 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1m22__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`1m22__assembly_2__model_1`	monomeric （1）	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 (3)

Entity 1 Entity 1 polymer

Description description	peptide amidase
Molecular weight formula_weight	53545.3 kDa
EC 编号 ec_number	3.5.1.-
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	8477

SRNVPFPYAETDVADLQARMTAGELDSTTLTQAYLQRIAALDRTGPRLRAVIELNPDALKEAAERDRERRDGRLRGPLHGIPLLLKDNINAAPMATSAGSLALQGFRPDDAYLVRRLRDAGAVVLGKTNLSEWANFRGNDSISGWSARGGQTRNPYRISHSPCGSSSGSAVAVAANLASVAIGTETDGSIVCPAAINGVVGLKPTVGLVSRDGIIPISFSQDTAGPMARSVADAAAVLTAIAGRDDADPATATMPGRAVYDYTARLDPQGLRGKRIGLLQTPLLKYRGMPPLIEQAATELRRAGAVVVPVELPNQGAWAEAERTLLLYEFKAGLERYFNTHRAPLRSLADLIAFNQAHSKQELGLFGQELLVEADATAGLADPAYIRARSDARRLAGPEGIDAALAAHQLDALVAPTTGVAWPIRSEGDDFPGESYSAAAVAGYPSLTVPMGQIDGLPVGLLFMGTAWSEPKLIEMAYAYEQRTRARRPPHFDTDALIDAGEP

Source Source

Source organism organism	Stenotrophomonas maltophilia
NCBI taxonomy ID ncbi_taxonomy_id	40324
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
Molecular weight formula_weight	238.3 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	1149

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6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d1m22a_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.117 — Amidase signature (AS) enzymes
Superfamily Superfamily superfamily	c.117.1 — Amidase signature (AS) enzymes
Family Family family	c.117.1.1 — Amidase signature (AS) enzymes

Domain ID domain_id	d1m22b_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.117 — Amidase signature (AS) enzymes
Superfamily Superfamily superfamily	c.117.1 — Amidase signature (AS) enzymes
Family Family family	c.117.1.1 — Amidase signature (AS) enzymes

CATH v4.4 (2 domains)

Domain ID domain_id	1m22A00
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	1300 — Amidase signature (AS) enzymes
Homologous superfamily homologous superfamily	10 — Amidase signature (AS) domain

Domain ID domain_id	1m22B00
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	1300 — Amidase signature (AS) enzymes
Homologous superfamily homologous superfamily	10 — Amidase signature (AS) domain

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Unit-cell length a length_a	74.179 Å
Unit-cell length b length_b	62.596 Å
Unit-cell length c length_c	101.906 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	4

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	1.400 Å
Low-resolution limit resolution_low	79.000 Å
R factor r_factor	0.1880
R_work r_work	0.1880
R_free r_free	0.1990

X-ray structure of native peptide amidase from Stenotrophomonas maltophilia at 1.4 A

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

peptide 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

1m22__assembly_1__model_1

1m22__assembly_1__model_1 | I(q)

1m22__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 (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) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (3)

X-ray structure of native peptide amidase from Stenotrophomonas maltophilia at 1.4 A

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

peptide 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

1m22__assembly_1__model_1

1m22__assembly_1__model_1 | I(q)

1m22__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 (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) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (3)