SAXSdb — 2rk9

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

Glyoxalase/bleomycin resistance protein/dioxygenase

Vibrio splendidus

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	A3UM69_VIBSP
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 4–137； UniProt 2–135 Author chain B； PDBConstruct 4–137； UniProt 2–135

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	2rk9
Deposition date deposition_date	2007-10-16
Structure title title	The crystal structure of a glyoxalase/bleomycin resistance protein/dioxygenase superfamily member from Vibrio splendidus 12B01
Keywords keywords	;11005r, Glyoxalase/bleomycin resistance protein/dioxygenase superfamily, NYSGXRC, Structural Genomics, Protein Structure Initiative II, New York SGX Research Center for Structural Genomics, PSI-2, OXIDOREDUCTASE ;; OXIDOREDUCTASE
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.

2rk9__assembly_1__model_1

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

Download this curve (.dat)

2rk9__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2rk9__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	18.91 Å
Rg (electron density)	17.62 Å
Total Rg	18.60 Å
Atom count	1905
Residues	229
Excluded volume	34142 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2rk9__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)

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6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d2rk9a_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.32 — Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase
Superfamily Superfamily superfamily	d.32.1 — Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase
Family Family family	d.32.1.0 — automated matches

Domain ID domain_id	d2rk9b_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.32 — Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase
Superfamily Superfamily superfamily	d.32.1 — Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase
Family Family family	d.32.1.0 — automated matches

CATH v4.4 (2 domains)

Domain ID domain_id	2rk9A00
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	180 — 2,3-Dihydroxybiphenyl 1,2-Dioxygenase; domain 1
Homologous superfamily homologous superfamily	10 — 2,3-Dihydroxybiphenyl 1,2-Dioxygenase, domain 1

Domain ID domain_id	2rk9B00
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	180 — 2,3-Dihydroxybiphenyl 1,2-Dioxygenase; domain 1
Homologous superfamily homologous superfamily	10 — 2,3-Dihydroxybiphenyl 1,2-Dioxygenase, domain 1

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Unit-cell length a length_a	40.704 Å
Unit-cell length b length_b	76.954 Å
Unit-cell length c length_c	42.395 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	92.00 °
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	1.600 Å
Low-resolution limit resolution_low	40.680 Å
R factor r_factor	0.2090
R_work r_work	0.2090
R_free r_free	0.2290

Description description	Glyoxalase/bleomycin resistance protein/dioxygenase
Molecular weight formula_weight	16854.4 kDa
Mutation mutation	I119M
Source method src_method	man
Copy count entity_count	2

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	2123

The crystal structure of a glyoxalase/bleomycin resistance protein/dioxygenase superfamily member from Vibrio splendidus 12B01

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

Glyoxalase/bleomycin resistance protein/dioxygenase

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

2rk9__assembly_1__model_1

2rk9__assembly_1__model_1 | I(q)

2rk9__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)

Source organism organism	Vibrio splendidus
NCBI taxonomy ID ncbi_taxonomy_id	314291
Host organism host_organism	Escherichia coli BL21(DE3)

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	218

The crystal structure of a glyoxalase/bleomycin resistance protein/dioxygenase superfamily member from Vibrio splendidus 12B01

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

Glyoxalase/bleomycin resistance protein/dioxygenase

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

2rk9__assembly_1__model_1

2rk9__assembly_1__model_1 | I(q)

2rk9__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)