SAXSdb — 3bpb

▼

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

dimethylarginine dimethylaminohydrolase

Pseudomonas aeruginosa

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	N~5~-[(E)-imino(methylsulfanyl)methyl]-L-ornithine × 1 water × 1	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	N~5~-[(E)-imino(methylsulfanyl)methyl]-L-ornithine × 1 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q9I4E3_PSEAE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–254； UniProt 1–254 Author chain B； PDBConstruct 1–254； UniProt 1–254

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	3bpb
Deposition date deposition_date	2007-12-18
Structure title title	Crystal structure of the dimethylarginine dimethylaminohydrolase H162G adduct with S-methyl-L-thiocitrulline
Keywords keywords	enzyme adduct, HYDROLASE; 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.

3bpb__assembly_1__model_1

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

Download this curve (.dat)

3bpb__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3bpb__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	18.17 Å
Rg (electron density)	16.95 Å
Total Rg	17.88 Å
Atom count	1996
Residues	254
Excluded volume	35456 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3bpb__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`3bpb__assembly_2__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	dimethylarginine dimethylaminohydrolase
Molecular weight formula_weight	28425.4 kDa
EC 编号 ec_number	3.5.3.18
Mutation mutation	H162G
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	4059

MFKHIIARTPARSLVDGLTSSHLGKPDYAKALEQHNAYIRALQTCDVDITLLPPDERFPDSVFVEDPVLCTSRCAIITRPGAESRRGETEIIEETVQRFYPGKVERIEAPGTVEAGDIMMVGDHFYIGESARTNAEGARQMIAILEKHGLSGSVVRLEKVLGLKTGLAYLEHNNLLAAGEFVSKPEFQDFNIIEIPEEESYAANCIWVNERVIMPAGYPRTREKIARLGYRVIEVDTSEYRKIDGGVSCMSLRF

Source Source

Source organism organism	Pseudomonas aeruginosa
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	N~5~-[(E)-imino(methylsulfanyl)methyl]-L-ornithine
Molecular weight formula_weight	205.3 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	59

▼

6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d3bpba_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.126 — Pentein, beta/alpha-propeller
Superfamily Superfamily superfamily	d.126.1 — Pentein
Family Family family	d.126.1.3 — Dimethylarginine dimethylaminohydrolase DDAH

Domain ID domain_id	d3bpbb_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.126 — Pentein, beta/alpha-propeller
Superfamily Superfamily superfamily	d.126.1 — Pentein
Family Family family	d.126.1.3 — Dimethylarginine dimethylaminohydrolase DDAH

CATH v4.4 (2 domains)

Domain ID domain_id	3bpbA00
Class class	3 — Alpha Beta
Architecture architecture	75 — 5-stranded Propeller
Topology topology	10 — L-arginine/glycine Amidinotransferase; Chain A
Homologous superfamily homologous superfamily	10 — L-arginine/glycine Amidinotransferase; Chain A

Domain ID domain_id	3bpbB00
Class class	3 — Alpha Beta
Architecture architecture	75 — 5-stranded Propeller
Topology topology	10 — L-arginine/glycine Amidinotransferase; Chain A
Homologous superfamily homologous superfamily	10 — L-arginine/glycine Amidinotransferase; Chain A

▶

Unit-cell length a length_a	86.258 Å
Unit-cell length b length_b	127.532 Å
Unit-cell length c length_c	47.339 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	2.810 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	—
R_work r_work	0.2330
R_free r_free	0.2970

Crystal structure of the dimethylarginine dimethylaminohydrolase H162G adduct with S-methyl-L-thiocitrulline

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

dimethylarginine dimethylaminohydrolase

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

3bpb__assembly_1__model_1

3bpb__assembly_1__model_1 | I(q)

3bpb__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 (1)

Crystal structure of the dimethylarginine dimethylaminohydrolase H162G adduct with S-methyl-L-thiocitrulline

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

dimethylarginine dimethylaminohydrolase

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

3bpb__assembly_1__model_1

3bpb__assembly_1__model_1 | I(q)

3bpb__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 (1)