2bp7

New crystal form of the Pseudomonas putida branched-chain dehydrogenase (E1)

Method: X-RAY DIFFRACTION

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

2-OXOISOVALERATE DEHYDROGENASE ALPHA SUBUNIT

PSEUDOMONAS PUTIDA

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	2-OXOISOVALERATE DEHYDROGENASE BETA SUBUNIT × 2 （P09061） water × 4	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 4	2-OXOISOVALERATE DEHYDROGENASE BETA SUBUNIT × 2 （P09061） water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	ODBA_PSEPU
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–410； UniProt 1–410 Author chain C； PDBConstruct 1–410； UniProt 1–410 Author chain E； PDBConstruct 1–410； UniProt 1–410 Author chain G； PDBConstruct 1–410； UniProt 1–410

2-OXOISOVALERATE DEHYDROGENASE BETA SUBUNIT

PSEUDOMONAS PUTIDA

UniProt P09061

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	2-OXOISOVALERATE DEHYDROGENASE ALPHA SUBUNIT × 2 （P09060） water × 4	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 4	2-OXOISOVALERATE DEHYDROGENASE ALPHA SUBUNIT × 2 （P09060） water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	ODBB_PSEPU
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–339； UniProt 1–339 Author chain D； PDBConstruct 1–339； UniProt 1–339 Author chain F； PDBConstruct 1–339； UniProt 1–339 Author chain H； PDBConstruct 1–339； UniProt 1–339

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	2bp7
Deposition date deposition_date	2005-04-18
Structure title title	New crystal form of the Pseudomonas putida branched-chain dehydrogenase (E1)
Keywords keywords	FLAVOPROTEIN, THDP COFACTOR, 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.

2bp7__assembly_1__model_1

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

Download this curve (.dat)

2bp7__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2bp7__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	32.87 Å
Rg (electron density)	31.65 Å
Total Rg	32.38 Å
Atom count	11490
Residues	1490
Excluded volume	202860 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2bp7__assembly_1__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`2bp7__assembly_2__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	2-OXOISOVALERATE DEHYDROGENASE ALPHA SUBUNIT
Molecular weight formula_weight	45319.0 kDa
EC 编号 ec_number	1.2.4.4
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,C,E,G
Atom count atom_count	23118

MNEYAPLRLHVPEPTGRPGCQTDFSYLRLNDAGQARKPPVDVDAADTADLSYSLVRVLDEQGDAQGPWAEDIDPQILRQGMRAMLKTRIFDSRMVVAQRQKKMSFYMQSLGEEAIGSGQALALNRTDMCFPTYRQQSILMARDVSLVEMICQLLSNERDPLKGRQLPIMYSVREAGFFTISGNLATQFVQAVGWAMASAIKGDTKIASAWIGDGATAESDFHTALTFAHVYRAPVILNVVNNQWAISTFQAIAGGESTTFAGRGVGCGIASLRVDGNDFVAVYAASRWAAERARRGLGPSLIEWVTYRAGPHSTSDDPSKYRPADDWSHFPLGDPIARLKQHLIKIGHWSEEEHQATTAEFEAAVIAAQKEAEQYGTLANGHIPSAASMFEDVYKEMPDHLRRQRQELGV

Source Source

Source organism organism	PSEUDOMONAS PUTIDA
NCBI taxonomy ID ncbi_taxonomy_id	303
Host organism host_organism	ESCHERICHIA COLI

Entity 2 Entity 2 polymer

Description description	2-OXOISOVALERATE DEHYDROGENASE BETA SUBUNIT
Molecular weight formula_weight	37172.2 kDa
EC 编号 ec_number	1.2.4.4
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,D,F,H

MATTTMTMIQALRSAMDVMLERDDNVVVYGQDVGYFGGVFRCTEGLQTKYGKSRVFDAPISESGIVGTAVGMGAYGLRPVVEIQFADYFYPASDQIVSEMARLRYRSAGEFIAPLTLRMPCGGGIYGGQTHSQSPEAMFTQVCGLRTVMPSNPYDAKGLLIASIECDDPVIFLEPKRLYNGPFDGHHDRPVTPWSKHPHSAVPDGYYTVPLDKAAITRPGNDVSVLTYGTTVYVAQVAAEESGVDAEVIDLRSLWPLDLDTIVESVKKTGRCVVVHEATRTCGFGAELVSLVQEHCFHHLEAPIERVTGWDTPYPHAQEWAYFPGPSRVGAALKKVMEV

Source Source

Source organism organism	PSEUDOMONAS PUTIDA
NCBI taxonomy ID ncbi_taxonomy_id	303
Host organism host_organism	ESCHERICHIA COLI

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	138

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6. Fold Classification (SCOP + CATH) 24 domains

SCOP 2.08 (12 domains)

Domain ID domain_id	d2bp7a_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.36 — Thiamin diphosphate-binding fold (THDP-binding)
Superfamily Superfamily superfamily	c.36.1 — Thiamin diphosphate-binding fold (THDP-binding)
Family Family family	c.36.1.11 — Branched-chain alpha-keto acid dehydrogenase PP module

Domain ID domain_id	d2bp7b1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.36 — Thiamin diphosphate-binding fold (THDP-binding)
Superfamily Superfamily superfamily	c.36.1 — Thiamin diphosphate-binding fold (THDP-binding)
Family Family family	c.36.1.7 — Branched-chain alpha-keto acid dehydrogenase Pyr module

Domain ID domain_id	d2bp7b2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.48 — TK C-terminal domain-like
Superfamily Superfamily superfamily	c.48.1 — TK C-terminal domain-like
Family Family family	c.48.1.2 — Branched-chain alpha-keto acid dehydrogenase beta-subunit, C-terminal-domain

Domain ID domain_id	d2bp7c_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.36 — Thiamin diphosphate-binding fold (THDP-binding)
Superfamily Superfamily superfamily	c.36.1 — Thiamin diphosphate-binding fold (THDP-binding)
Family Family family	c.36.1.11 — Branched-chain alpha-keto acid dehydrogenase PP module

Domain ID domain_id	d2bp7d1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.36 — Thiamin diphosphate-binding fold (THDP-binding)
Superfamily Superfamily superfamily	c.36.1 — Thiamin diphosphate-binding fold (THDP-binding)
Family Family family	c.36.1.7 — Branched-chain alpha-keto acid dehydrogenase Pyr module

Domain ID domain_id	d2bp7d2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.48 — TK C-terminal domain-like
Superfamily Superfamily superfamily	c.48.1 — TK C-terminal domain-like
Family Family family	c.48.1.2 — Branched-chain alpha-keto acid dehydrogenase beta-subunit, C-terminal-domain

Domain ID domain_id	d2bp7e_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.36 — Thiamin diphosphate-binding fold (THDP-binding)
Superfamily Superfamily superfamily	c.36.1 — Thiamin diphosphate-binding fold (THDP-binding)
Family Family family	c.36.1.11 — Branched-chain alpha-keto acid dehydrogenase PP module

Domain ID domain_id	d2bp7f1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.36 — Thiamin diphosphate-binding fold (THDP-binding)
Superfamily Superfamily superfamily	c.36.1 — Thiamin diphosphate-binding fold (THDP-binding)
Family Family family	c.36.1.7 — Branched-chain alpha-keto acid dehydrogenase Pyr module

Domain ID domain_id	d2bp7f2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.48 — TK C-terminal domain-like
Superfamily Superfamily superfamily	c.48.1 — TK C-terminal domain-like
Family Family family	c.48.1.2 — Branched-chain alpha-keto acid dehydrogenase beta-subunit, C-terminal-domain

Domain ID domain_id	d2bp7g_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.36 — Thiamin diphosphate-binding fold (THDP-binding)
Superfamily Superfamily superfamily	c.36.1 — Thiamin diphosphate-binding fold (THDP-binding)
Family Family family	c.36.1.11 — Branched-chain alpha-keto acid dehydrogenase PP module

Domain ID domain_id	d2bp7h1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.36 — Thiamin diphosphate-binding fold (THDP-binding)
Superfamily Superfamily superfamily	c.36.1 — Thiamin diphosphate-binding fold (THDP-binding)
Family Family family	c.36.1.7 — Branched-chain alpha-keto acid dehydrogenase Pyr module

Domain ID domain_id	d2bp7h2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.48 — TK C-terminal domain-like
Superfamily Superfamily superfamily	c.48.1 — TK C-terminal domain-like
Family Family family	c.48.1.2 — Branched-chain alpha-keto acid dehydrogenase beta-subunit, C-terminal-domain

CATH v4.4 (12 domains)

Domain ID domain_id	2bp7A00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	970 — Thiamin diphosphate (ThDP)-binding fold, Pyr/PP domains

Domain ID domain_id	2bp7B01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	970 — Thiamin diphosphate (ThDP)-binding fold, Pyr/PP domains

Domain ID domain_id	2bp7B02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	920 —

Domain ID domain_id	2bp7C00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	970 — Thiamin diphosphate (ThDP)-binding fold, Pyr/PP domains

Domain ID domain_id	2bp7D01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	970 — Thiamin diphosphate (ThDP)-binding fold, Pyr/PP domains

Domain ID domain_id	2bp7D02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	920 —

Domain ID domain_id	2bp7E00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	970 — Thiamin diphosphate (ThDP)-binding fold, Pyr/PP domains

Domain ID domain_id	2bp7F01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	970 — Thiamin diphosphate (ThDP)-binding fold, Pyr/PP domains

Domain ID domain_id	2bp7F02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	920 —

Domain ID domain_id	2bp7G00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	970 — Thiamin diphosphate (ThDP)-binding fold, Pyr/PP domains

Domain ID domain_id	2bp7H01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	970 — Thiamin diphosphate (ThDP)-binding fold, Pyr/PP domains

Domain ID domain_id	2bp7H02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	920 —

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Unit-cell length a length_a	156.866 Å
Unit-cell length b length_b	156.866 Å
Unit-cell length c length_c	619.605 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	48

Space group space_group	P 61 2 2
Space-group number int_tables_number	178
Crystal system crystal_system	—

Resolution resolution	2.900 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	0.2280
R_work r_work	0.2270
R_free r_free	0.2540

New crystal form of the Pseudomonas putida branched-chain dehydrogenase (E1)

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

2-OXOISOVALERATE DEHYDROGENASE ALPHA SUBUNIT

State in the Current Structure

Other States of the Same Protein in the Database

2-OXOISOVALERATE DEHYDROGENASE BETA SUBUNIT

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

2bp7__assembly_1__model_1

2bp7__assembly_1__model_1 | I(q)

2bp7__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 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 24 domains

SCOP 2.08 (12 domains)

CATH v4.4 (12 domains)

7. Citations (1)

New crystal form of the Pseudomonas putida branched-chain dehydrogenase (E1)

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

2-OXOISOVALERATE DEHYDROGENASE ALPHA SUBUNIT

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-OXOISOVALERATE DEHYDROGENASE BETA SUBUNIT

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

2bp7__assembly_1__model_1

2bp7__assembly_1__model_1 | I(q)

2bp7__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 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 24 domains

SCOP 2.08 (12 domains)

CATH v4.4 (12 domains)

7. Citations (1)