SAXSdb — 2dkg

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

235aa long hypothetical biotin-[acetyl-CoA-carboxylase] ligase

Pyrococcus horikoshii

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	MAGNESIUM ION × 1 PYROPHOSPHATE 2- × 1 BIOTINYL-5-AMP × 2 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	O57883_PYRHO
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–235； UniProt 1–235 Author chain B； PDBConstruct 1–235； UniProt 1–235

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	2dkg
Deposition date deposition_date	2006-04-11
Structure title title	Crystal Structure Of Biotin Protein Ligase From Pyrococcus Horikoshii OT3 in Complex with Biotinyl-5'-AMP, Pyrophosphate and Mg(2+)
Keywords keywords	;Biotin Biosynthesis, Dimer, Structural Genomics, NPPSFA, National Project on Protein Structural and Functional Analyses, RIKEN Structural Genomics/Proteomics Initiative, RSGI, LIGASE ;; LIGASE
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.

2dkg__assembly_1__model_1

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

Download this curve (.dat)

2dkg__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2dkg__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	27.74 Å
Rg (electron density)	27.35 Å
Total Rg	27.88 Å
Atom count	3760
Residues	470
Excluded volume	68118 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2dkg__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 (5)

Entity 1 Entity 1 polymer

Description description	235aa long hypothetical biotin-[acetyl-CoA-carboxylase] ligase
Molecular weight formula_weight	26103.5 kDa
EC 编号 ec_number	6.3.4.15
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	4155

MLGLKTSIIGRRVIYFQEITSTNEFAKTSYLEEGTVIVADKQTMGHGRLNRKWESPEGGLWLSIVLSPKVPQKDLPKIVFLGAVGVVETLKEFSIDGRIKWPNDVLVNYKKIAGVLVEGKGDKIVLGIGLNVNNKVPNGATSMKLELGSEVPLLSVFRSLITNLDRLYLNFLKNPMDILNLVRDNMILGVRVKILGDGSFEGIAEDIDDFGRLIIRLDSGEVKKVIYGDVSLRFL

Source Source

Source organism organism	Pyrococcus horikoshii
NCBI taxonomy ID ncbi_taxonomy_id	70601
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 non-polymer

Description description	PYROPHOSPHATE 2-
Molecular weight formula_weight	176.0 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	BIOTINYL-5-AMP
Molecular weight formula_weight	573.5 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	395

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6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d2dkga1
Class class	b — All beta proteins
Fold Fold fold	b.34 — SH3-like barrel
Superfamily Superfamily superfamily	b.34.1 — C-terminal domain of transcriptional repressors
Family Family family	b.34.1.1 — Biotin repressor (BirA)

Domain ID domain_id	d2dkga2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.104 — Class II aaRS and biotin synthetases
Superfamily Superfamily superfamily	d.104.1 — Class II aaRS and biotin synthetases
Family Family family	d.104.1.2 — Biotin holoenzyme synthetase

Domain ID domain_id	d2dkgb1
Class class	b — All beta proteins
Fold Fold fold	b.34 — SH3-like barrel
Superfamily Superfamily superfamily	b.34.1 — C-terminal domain of transcriptional repressors
Family Family family	b.34.1.1 — Biotin repressor (BirA)

Domain ID domain_id	d2dkgb2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.104 — Class II aaRS and biotin synthetases
Superfamily Superfamily superfamily	d.104.1 — Class II aaRS and biotin synthetases
Family Family family	d.104.1.2 — Biotin holoenzyme synthetase

CATH v4.4 (4 domains)

Domain ID domain_id	2dkgA01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	930 — BirA Bifunctional Protein; domain 2
Homologous superfamily homologous superfamily	10 — Bira Bifunctional Protein; Domain 2

Domain ID domain_id	2dkgA02
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	30 — SH3 type barrels.
Homologous superfamily homologous superfamily	100 —

Domain ID domain_id	2dkgB01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	930 — BirA Bifunctional Protein; domain 2
Homologous superfamily homologous superfamily	10 — Bira Bifunctional Protein; Domain 2

Domain ID domain_id	2dkgB02
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	30 — SH3 type barrels.
Homologous superfamily homologous superfamily	100 —

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Unit-cell length a length_a	38.320 Å
Unit-cell length b length_b	82.721 Å
Unit-cell length c length_c	72.373 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	101.81 °
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	2.000 Å
Low-resolution limit resolution_low	32.560 Å
R factor r_factor	0.1890
R_work r_work	0.1890
R_free r_free	0.2230

Crystal Structure Of Biotin Protein Ligase From Pyrococcus Horikoshii OT3 in Complex with Biotinyl-5'-AMP, Pyrophosphate and Mg(2+)

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

235aa long hypothetical biotin-[acetyl-CoA-carboxylase] ligase

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

2dkg__assembly_1__model_1

2dkg__assembly_1__model_1 | I(q)

2dkg__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 (5)

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 water

6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

7. Citations (1)

Crystal Structure Of Biotin Protein Ligase From Pyrococcus Horikoshii OT3 in Complex with Biotinyl-5'-AMP, Pyrophosphate and Mg(2+)

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

235aa long hypothetical biotin-[acetyl-CoA-carboxylase] ligase

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

2dkg__assembly_1__model_1

2dkg__assembly_1__model_1 | I(q)

2dkg__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 (5)

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 water

6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

7. Citations (1)