SAXSdb — 1och

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

MALONAMIDASE E2

BRADYRHIZOBIUM JAPONICUM

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q9ZIV5
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–414； UniProt 1–414 Author chain B； PDBConstruct 1–414； UniProt 1–414

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	1och
Deposition date deposition_date	2003-02-07
Structure title title	Crystal structure of the S155C mutant of malonamidase E2 from Bradyrhizobium japonicum
Keywords keywords	AMIDASE, MALONAMIDASE, MUTANT; AMIDASE
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.

1och__assembly_1__model_1

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

Download this curve (.dat)

1och__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1och__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	27.86 Å
Rg (electron density)	26.91 Å
Total Rg	27.68 Å
Atom count	6130
Residues	824
Excluded volume	108600 Å³
Maximum q	0.500 Å⁻¹

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

Entity 1 Entity 1 polymer

Description description	MALONAMIDASE E2
Molecular weight formula_weight	43783.8 kDa
Mutation mutation	YES
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	7011

MISLADLQRRIETGELSPNAAIAQSHAAIEAREKEVHAFVRHDKSARAQASGPLRGIAVGIKDIIDTANMPTEMGSEIYRGWQPRSDAPVVMMLKRAGATIIGKTTTTAFASRDPTATLNPHNTGHSPGGSSSGSAAAVGAGMIPLALGTQTGGCVIRPAAYCGTAAIKPSFRMLPTVGVKCYSWALDTVGLFGARAEDLARGLLAMTGRSEFSGIVPAKAPRIGVVRQEFAGAVEPAAEQGLQAAIKAAERAGASVQAIDLPEAVHEAWRIHPIIQDFEAHRALAWEFSEHHDEIAPMLRASLDATVGLTPKEYDEARRIGRRGRRELGEVFEGVDVLLTYSAPGTAPAKALASTGDPRYNRLWTLMGNPCVNVPVLKVGGLPIGVQVIARFGNDAHALATAWFLEDALAKSG

Source Source

Source organism organism	BRADYRHIZOBIUM JAPONICUM
Common name common_name	BACTEROID
NCBI taxonomy ID ncbi_taxonomy_id	375
Host organism host_organism	ESCHERICHIA COLI

Entity 2 Entity 2 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	881

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6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d1ocha_
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	d1ochb_
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	1ochA00
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	1ochB00
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	103.606 Å
Unit-cell length b length_b	94.985 Å
Unit-cell length c length_c	74.921 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	8

Space group space_group	P 21 21 2
Space-group number int_tables_number	18
Crystal system crystal_system	—

Resolution resolution	1.800 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	0.1940
R_work r_work	0.1940
R_free r_free	0.2370

Crystal structure of the S155C mutant of malonamidase E2 from Bradyrhizobium japonicum

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

MALONAMIDASE E2

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

1och__assembly_1__model_1

1och__assembly_1__model_1 | I(q)

1och__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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 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 S155C mutant of malonamidase E2 from Bradyrhizobium japonicum

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

MALONAMIDASE E2

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

1och__assembly_1__model_1

1och__assembly_1__model_1 | I(q)

1och__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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 water

6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)