SAXSdb — 2bdr

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

Ureidoglycolate hydrolase

Pseudomonas putida

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	SODIUM ION × 3 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	ALLA_PSEPK
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–167； UniProt 1–167 Author chain B； PDBConstruct 1–167； UniProt 1–167

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	2bdr
Deposition date deposition_date	2005-10-20
Structure title title	Crystal Structure of the Putative Ureidoglycolate hydrolase PP4288 from Pseudomonas putida, Northeast Structural Genomics Target PpR49
Keywords keywords	all beta protein, Structural Genomics, PSI, Protein Structure Initiative, Northeast Structural Genomics Consortium, NESG, 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.

2bdr__assembly_1__model_1

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

Download this curve (.dat)

2bdr__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2bdr__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	22.15 Å
Rg (electron density)	21.19 Å
Total Rg	22.39 Å
Atom count	2623
Residues	318
Excluded volume	46658 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2bdr__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 (3)

Entity 1 Entity 1 polymer

Description description	Ureidoglycolate hydrolase
Molecular weight formula_weight	20190.8 kDa
EC 编号 ec_number	3.5.3.19
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	2958

MRTLMIEPLTKEAFAQFGDVIETDGSDHFMINNGSTMRFHKLATVETAEPEDKAIISIFRADAQDMPLTVRMLERHPLGSQAFIPLLGNPFLIVVAPVGDAPVSGLVRAFRSNGRQGVNYHRGVWHHPVLTIEKRDDFLVVDRSGSGNNCDEHYFTEEQMLILNPHQLEHHHHHH

Source Source

Source organism organism	Pseudomonas putida
NCBI taxonomy ID ncbi_taxonomy_id	160488
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	SODIUM ION
Molecular weight formula_weight	23.0 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	335

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6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d2bdra1
Class class	b — All beta proteins
Fold Fold fold	b.82 — Double-stranded beta-helix
Superfamily Superfamily superfamily	b.82.1 — RmlC-like cupins
Family Family family	b.82.1.14 — Ureidoglycolate hydrolase AllA

Domain ID domain_id	d2bdrb_
Class class	b — All beta proteins
Fold Fold fold	b.82 — Double-stranded beta-helix
Superfamily Superfamily superfamily	b.82.1 — RmlC-like cupins
Family Family family	b.82.1.14 — Ureidoglycolate hydrolase AllA

CATH v4.4 (2 domains)

Domain ID domain_id	2bdrA00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	480 — Ureidoglycolate hydrolase

Domain ID domain_id	2bdrB00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	480 — Ureidoglycolate hydrolase

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Unit-cell length a length_a	83.027 Å
Unit-cell length b length_b	55.268 Å
Unit-cell length c length_c	81.843 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	93.98 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

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

Resolution resolution	1.600 Å
Low-resolution limit resolution_low	31.130 Å
R factor r_factor	0.1980
R_work r_work	0.1980
R_free r_free	0.2180

Crystal Structure of the Putative Ureidoglycolate hydrolase PP4288 from Pseudomonas putida, Northeast Structural Genomics Target PpR49

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

Ureidoglycolate hydrolase

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

2bdr__assembly_1__model_1

2bdr__assembly_1__model_1 | I(q)

2bdr__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 Putative Ureidoglycolate hydrolase PP4288 from Pseudomonas putida, Northeast Structural Genomics Target PpR49

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

Ureidoglycolate hydrolase

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

2bdr__assembly_1__model_1

2bdr__assembly_1__model_1 | I(q)

2bdr__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)