SAXSdb — 2p8i

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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	CHLORIDE ION × 3 PHOSPHATE ION × 2 1,2-ETHANEDIOL × 2 water × 2	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 2	CHLORIDE ION × 1 PHOSPHATE ION × 2 1,2-ETHANEDIOL × 3 CITRIC ACID × 1 water × 2	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 Author chain C； PDBConstruct 2–117； UniProt 1–116 Author chain D； 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	2p8i
Deposition date deposition_date	2007-03-22
Structure title title	Crystal structure of putative dioxygenase (YP_555069.1) from Burkholderia xenovorans LB400 at 1.40 A resolution
Keywords keywords	;YP_555069.1, putative dioxygenase, Structural Genomics, Joint Center for Structural Genomics, JCSG, Protein Structure Initiative, 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.

2p8i__assembly_2__model_1

Assembly 2 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

2p8i__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2p8i__assembly_2__model_1 | P(r) · Pending

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

Rg（Guinier）	18.49 Å
Rg (electron density)	17.29 Å
Total Rg	18.30 Å
Atom count	1915
Residues	229
Excluded volume	33389 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2p8i__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`2p8i__assembly_2__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 (6)

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	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	4786

GMTFRDTSAIASWHAHVYFDASSRDAAWTLREQIEAHWSGKLQLGRFHERPVGPHPMWSYQLAFTQEQFADLVGWLTLNHGALDIFLHPNTGDALRDHRDAAVWIGHSHELVLSALN

Source Source

Source organism organism	Burkholderia xenovorans
NCBI taxonomy ID ncbi_taxonomy_id	266265
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 3 Entity 3 non-polymer

Description description	PHOSPHATE ION
Molecular weight formula_weight	95.0 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 4 Entity 4 non-polymer

Description description	1,2-ETHANEDIOL
Molecular weight formula_weight	62.1 kDa
Source method src_method	syn
Copy count entity_count	5

Entity 5 Entity 5 non-polymer

Description description	CITRIC ACID
Molecular weight formula_weight	192.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	877

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6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (8 domains)

Domain ID domain_id	d2p8ia2
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	d2p8ia3
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	d2p8ib2
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	d2p8ib3
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	d2p8ic2
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	d2p8ic3
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	d2p8id2
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	d2p8id3
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

CATH v4.4 (4 domains)

Domain ID domain_id	2p8iA00
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	2p8iB00
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	2p8iC00
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	2p8iD00
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	43.835 Å
Unit-cell length b length_b	138.772 Å
Unit-cell length c length_c	44.046 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	98.43 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	1.400 Å
Low-resolution limit resolution_low	30.002 Å
R factor r_factor	0.1450
R_work r_work	0.1440
R_free r_free	0.1730

Crystal structure of putative dioxygenase (YP_555069.1) from Burkholderia xenovorans LB400 at 1.40 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

2p8i__assembly_2__model_1

2p8i__assembly_2__model_1 | I(q)

2p8i__assembly_2__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 (6)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (8 domains)

CATH v4.4 (4 domains)

7. Citations (1)

Crystal structure of putative dioxygenase (YP_555069.1) from Burkholderia xenovorans LB400 at 1.40 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

2p8i__assembly_2__model_1

2p8i__assembly_2__model_1 | I(q)

2p8i__assembly_2__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 (6)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (8 domains)

CATH v4.4 (4 domains)

7. Citations (1)