1wnb

Escherichia coli YdcW gene product is a medium-chain aldehyde dehydrogenase (complexed with nadh and betaine aldehyde)

Method: X-RAY DIFFRACTION

▼

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

Putative betaine aldehyde dehydrogenase

Escherichia coli

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 4	1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE × 4 BETAINE ALDEHYDE × 1 water × 4	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 4	1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE × 4 BETAINE ALDEHYDE × 1 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	YDCW_ECOLI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 22–495； UniProt 1–474 Author chain B； PDBConstruct 22–495； UniProt 1–474 Author chain C； PDBConstruct 22–495； UniProt 1–474 Author chain D； PDBConstruct 22–495； UniProt 1–474

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	1wnb
Deposition date deposition_date	2004-07-29
Structure title title	Escherichia coli YdcW gene product is a medium-chain aldehyde dehydrogenase (complexed with nadh and betaine aldehyde)
Keywords keywords	aldehyde dehydrogenase, NADH, flurorescence, kinetics, OXIDOREDUCTASE; OXIDOREDUCTASE
Experimental Method method	X-RAY DIFFRACTION

▼

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.

1wnb__assembly_2__model_1

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

Download this curve (.dat)

1wnb__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1wnb__assembly_2__model_1 | P(r) · Pending

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

Rg（Guinier）	42.26 Å
Rg (electron density)	42.01 Å
Total Rg	42.31 Å
Atom count	14483
Residues	1896
Excluded volume	257390 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1wnb__assembly_1__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`1wnb__assembly_2__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download

▶

4. Crystallography and Experiment 4. Crystallography & Experiment

▶

5. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	Putative betaine aldehyde dehydrogenase
Molecular weight formula_weight	53409.6 kDa
EC 编号 ec_number	1.2.1.8
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	15318

SYYHHHHHHLESTSLYKKAGLMQHKLLINGELVSGEGEKQPVYNPATGDVLLEIAEASAEQVDAAVRAADAAFAEWGQTTPKVRAECLLKLADVIEENGQVFAELESRNCGKPLHSAFNDEIPAIVDVFRFFAGAARCLNGLAAGEYLEGHTSMIRRDPLGVVASIAPWNYPLMMAAWKLAPALAAGNCVVLKPSEITPLTALKLAELAKDIFPAGVVNILFGRGKTVGDPLTGHPKVRMVSLTGSIATGEHIISHTASSIKRTHMELGGKAPVIVFDDADIEAVVEGVRTFGYYNAGQDCTAACRIYAQKGIYDTLVEKLGAAVATLKSGAPDDESTELGPLSSLAHLERVGKAVEEAKATGHIKVITGGEKRKGNGYYYAPTLLAGALQDDAIVQKEVFGPVVSVTPFDNEEQVVNWANDSQYGLASSVWTKDVGRAHRVSARLQYGCTWVNTHFMLVSEMPHGGQKLSGYGKDMSLYGLEDYTVVRHVMVKH

Source Source

Source organism organism	Escherichia coli
NCBI taxonomy ID ncbi_taxonomy_id	83333
Host organism host_organism	Escherichia coli BL21

Entity 2 Entity 2 non-polymer

Description description	1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE
Molecular weight formula_weight	665.4 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 3 Entity 3 non-polymer

Description description	BETAINE ALDEHYDE
Molecular weight formula_weight	102.2 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	831

▼

6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d1wnba_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.82 — ALDH-like
Superfamily Superfamily superfamily	c.82.1 — ALDH-like
Family Family family	c.82.1.1 — ALDH-like

Domain ID domain_id	d1wnbb_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.82 — ALDH-like
Superfamily Superfamily superfamily	c.82.1 — ALDH-like
Family Family family	c.82.1.1 — ALDH-like

Domain ID domain_id	d1wnbc_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.82 — ALDH-like
Superfamily Superfamily superfamily	c.82.1 — ALDH-like
Family Family family	c.82.1.1 — ALDH-like

Domain ID domain_id	d1wnbd_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.82 — ALDH-like
Superfamily Superfamily superfamily	c.82.1 — ALDH-like
Family Family family	c.82.1.1 — ALDH-like

CATH v4.4 (8 domains)

Domain ID domain_id	1wnbA01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	605 — Aldehyde Dehydrogenase; Chain A, domain 1
Homologous superfamily homologous superfamily	10 — Aldehyde Dehydrogenase; Chain A, domain 1

Domain ID domain_id	1wnbA02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	309 — Aldehyde Dehydrogenase; Chain A, domain 2
Homologous superfamily homologous superfamily	10 — Aldehyde Dehydrogenase; Chain A, domain 2

Domain ID domain_id	1wnbB01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	605 — Aldehyde Dehydrogenase; Chain A, domain 1
Homologous superfamily homologous superfamily	10 — Aldehyde Dehydrogenase; Chain A, domain 1

Domain ID domain_id	1wnbB02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	309 — Aldehyde Dehydrogenase; Chain A, domain 2
Homologous superfamily homologous superfamily	10 — Aldehyde Dehydrogenase; Chain A, domain 2

Domain ID domain_id	1wnbC01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	605 — Aldehyde Dehydrogenase; Chain A, domain 1
Homologous superfamily homologous superfamily	10 — Aldehyde Dehydrogenase; Chain A, domain 1

Domain ID domain_id	1wnbC02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	309 — Aldehyde Dehydrogenase; Chain A, domain 2
Homologous superfamily homologous superfamily	10 — Aldehyde Dehydrogenase; Chain A, domain 2

Domain ID domain_id	1wnbD01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	605 — Aldehyde Dehydrogenase; Chain A, domain 1
Homologous superfamily homologous superfamily	10 — Aldehyde Dehydrogenase; Chain A, domain 1

Domain ID domain_id	1wnbD02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	309 — Aldehyde Dehydrogenase; Chain A, domain 2
Homologous superfamily homologous superfamily	10 — Aldehyde Dehydrogenase; Chain A, domain 2

▶

Unit-cell length a length_a	80.278 Å
Unit-cell length b length_b	168.895 Å
Unit-cell length c length_c	85.476 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.65 °
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	2.200 Å
Low-resolution limit resolution_low	18.000 Å
R factor r_factor	0.1866
R_work r_work	0.1820
R_free r_free	0.2385

Escherichia coli YdcW gene product is a medium-chain aldehyde dehydrogenase (complexed with nadh and betaine aldehyde)

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

Putative betaine aldehyde dehydrogenase

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

1wnb__assembly_2__model_1

1wnb__assembly_2__model_1 | I(q)

1wnb__assembly_2__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

5. Entities and Polymers Entities & Polymers (4)

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 water

6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (4 domains)

CATH v4.4 (8 domains)

7. Citations (1)

Escherichia coli YdcW gene product is a medium-chain aldehyde dehydrogenase (complexed with nadh and betaine aldehyde)

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

Putative betaine aldehyde dehydrogenase

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

1wnb__assembly_2__model_1

1wnb__assembly_2__model_1 | I(q)

1wnb__assembly_2__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

5. Entities and Polymers Entities & Polymers (4)

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 water

6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (4 domains)

CATH v4.4 (8 domains)

7. Citations (1)