SAXSdb — 2nyh

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

Putative dioxygenase

Burkholderia xenovorans

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	SULFATE ION × 5 water × 2	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 4	SULFATE ION × 10 water × 4	Consistent with protein count
3	Protein homooligomer	Homooligomer	Protein 4	SULFATE ION × 10 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q13JM0_BURXL
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–117； UniProt 1–116 Author chain B； PDBConstruct 2–117； UniProt 1–116

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	2nyh
Deposition date deposition_date	2006-11-20
Structure title title	Crystal structure of putative dioxygenase (YP_555069.1) from Burkholderia Xenovorans LB400 at 1.70 A resolution
Keywords keywords	;YP_555069.1, putative Dioxygenase, Structural Genomics, PSI-2, Protein Structure Initiative, Joint Center for Structural Genomics, JCSG, 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.

2nyh__assembly_3__model_1

Assembly 3 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

2nyh__assembly_3__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2nyh__assembly_3__model_1 | P(r) · Pending

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

Rg（Guinier）	30.20 Å
Rg (electron density)	29.82 Å
Total Rg	30.35 Å
Atom count	3790
Residues	454
Excluded volume	65937 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2nyh__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`2nyh__assembly_2__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`2nyh__assembly_3__model_1`	tetrameric （4）	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	Putative dioxygenase
Molecular weight formula_weight	13423.6 kDa
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	2272

GMTFRDTSAIASWHAHVYFDASSRDAAWTLREQIEAHWSGKLQLGRFHERPVGPHPMWSYQLAFTQEQFADLVGWLTLNHGALDIFLHPNTGDALRDHRDAAVWIGHSHELVLSALN

Source Source

Source organism organism	Burkholderia xenovorans
NCBI taxonomy ID ncbi_taxonomy_id	36873
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	5

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	363

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6. Fold Classification (SCOP + CATH) 5 domains

SCOP 2.08 (3 domains)

Domain ID domain_id	d2nyha1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.58 — Ferredoxin-like
Superfamily Superfamily superfamily	d.58.55 — DOPA-like
Family Family family	d.58.55.1 — DOPA dioxygenase-like

Domain ID domain_id	d2nyha2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d2nyhb_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.58 — Ferredoxin-like
Superfamily Superfamily superfamily	d.58.55 — DOPA-like
Family Family family	d.58.55.1 — DOPA dioxygenase-like

CATH v4.4 (2 domains)

Domain ID domain_id	2nyhA00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	1240 — DOPA-like domains

Domain ID domain_id	2nyhB00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	1240 — DOPA-like domains

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Unit-cell length a length_a	70.970 Å
Unit-cell length b length_b	88.304 Å
Unit-cell length c length_c	88.571 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	16

Space group space_group	C 2 2 21
Space-group number int_tables_number	20
Crystal system crystal_system	—

Resolution resolution	1.700 Å
Low-resolution limit resolution_low	27.692 Å
R factor r_factor	0.1790
R_work r_work	0.1760
R_free r_free	0.2200

Crystal structure of putative dioxygenase (YP_555069.1) from Burkholderia Xenovorans LB400 at 1.70 A resolution

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

Putative 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

2nyh__assembly_3__model_1

2nyh__assembly_3__model_1 | I(q)

2nyh__assembly_3__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) 5 domains

SCOP 2.08 (3 domains)

CATH v4.4 (2 domains)

7. Citations (1)

Crystal structure of putative dioxygenase (YP_555069.1) from Burkholderia Xenovorans LB400 at 1.70 A resolution

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

Putative 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

2nyh__assembly_3__model_1

2nyh__assembly_3__model_1 | I(q)

2nyh__assembly_3__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) 5 domains

SCOP 2.08 (3 domains)

CATH v4.4 (2 domains)

7. Citations (1)