6nd3

wild-type choline TMA lyase in complex with betaine aldehyde

Method: X-RAY DIFFRACTION

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

Choline trimethylamine-lyase

Desulfovibrio alaskensis (strain G20)

State in the Current Structure

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

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	CUTC_DESAG
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 22–849； UniProt 19–846 Author chain B； PDBConstruct 22–849； UniProt 19–846 Author chain C； PDBConstruct 22–849； UniProt 19–846 Author chain D； PDBConstruct 22–849； UniProt 19–846 Author chain E； PDBConstruct 22–849； UniProt 19–846 Author chain F； PDBConstruct 22–849； UniProt 19–846 Author chain G； PDBConstruct 22–849； UniProt 19–846 Author chain H； PDBConstruct 22–849； UniProt 19–846

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	6nd3
Deposition date deposition_date	2018-12-13
Structure title title	wild-type choline TMA lyase in complex with betaine aldehyde
Keywords keywords	radical, lyase, barrel; LYASE
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.

6nd3__assembly_4__model_1

Assembly 4 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

6nd3__assembly_4__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

6nd3__assembly_4__model_1 | P(r) · Pending

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

Rg（Guinier）	39.29 Å
Rg (electron density)	39.14 Å
Total Rg	39.45 Å
Atom count	12547
Residues	1590
Excluded volume	223070 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`6nd3__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`6nd3__assembly_2__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`6nd3__assembly_3__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`6nd3__assembly_4__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
5	1	`6nd3__assembly_5__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download
6	1	`6nd3__assembly_6__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	Choline trimethylamine-lyase
Molecular weight formula_weight	95003.0 kDa
EC 编号 ec_number	4.3.99.4
Source method src_method	man
Copy count entity_count	8

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F,G,H
Atom count atom_count	52117

MGSSHHHHHHSSGLVPRGSHMPAERASLKKIFEGVSAEVFSQPAPVSAVATGAESGIPDGPTPRHVKLKENFLKQVPSITVQRAVAITKIAKENPGLPKPLLRAKTFRYCCETAPLVIQDHELIVGSPNGAPRAGAFSPEVAWRWLQDELDTIGSRPQDPFYISEEDKKVLREEVFPFWQNKSVDEFCEGQYREADLWEMSGESFVSDCSYHAVNGGGDSNPGYDVILMKKGMLDIQREAREKLEQLDYANPEDIDKIYFYKSVIETAEGVMIYARRLSAYAAELAARETDPRRKAELQKISEVNARVPAHAPSNFWEAIQAVWTVESLLVVEENQTGMSIGRVDQYMYPFYRADIDSGRLTEYEAFDLAGCMLVKMSEMMWITSEGASKFFAGYQPFVNMCVGGVTREGHDATNDLTYMLMDAVRHVRIYQPTLATRVHNKSPQKYLKKIVDVIRSGMGFPAVHFDDAHIKMMLAKGVSIEDARDYCLMGCVEPQKSGRLYQWTSTGYTQWPICIELVLNHGVPLWYGKKVTPDMGDLSQYDTYEKFEAAVKEQIRWITKNTSVATVISQRAHRELAPKPLMSLMYEGCMESGRDVSAGGAMYNFGPGVVWSGLATYVDSMAAIKKLVYDDRKYTLAQLNEALKADFAGYDQILADCLAAPKYGNDDDYADMIAADLVHFTETEHRKYKTLYSVLSHGTLSISNNTPFGQLLGASANGRRAWMPLSDGISPTQGADYKGPTAIIKSVSKMANDNMNIGMVHNFKLMSGLLDTPEGENGLITLIRTACMLGNGEMQFNYLDNELLLDAQKHPEKYRDLVVRVAGYSAFFVELCKDVQDEIISRTMLHGF

Source Source

Source organism organism	Desulfovibrio alaskensis (strain G20)
Common name common_name	Desulfovibrio desulfuricans (strain G20)
NCBI taxonomy ID ncbi_taxonomy_id	207559
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 non-polymer

Description description	BETAINE ALDEHYDE
Molecular weight formula_weight	102.2 kDa
Source method src_method	syn
Copy count entity_count	8

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	1813

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6. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

Domain ID domain_id	d6nd3a_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.7 — PFL-like glycyl radical enzymes
Superfamily Superfamily superfamily	c.7.1 — PFL-like glycyl radical enzymes
Family Family family	c.7.1.0 — automated matches

Domain ID domain_id	d6nd3b_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.7 — PFL-like glycyl radical enzymes
Superfamily Superfamily superfamily	c.7.1 — PFL-like glycyl radical enzymes
Family Family family	c.7.1.0 — automated matches

Domain ID domain_id	d6nd3c_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.7 — PFL-like glycyl radical enzymes
Superfamily Superfamily superfamily	c.7.1 — PFL-like glycyl radical enzymes
Family Family family	c.7.1.0 — automated matches

Domain ID domain_id	d6nd3d_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.7 — PFL-like glycyl radical enzymes
Superfamily Superfamily superfamily	c.7.1 — PFL-like glycyl radical enzymes
Family Family family	c.7.1.0 — automated matches

Domain ID domain_id	d6nd3e_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.7 — PFL-like glycyl radical enzymes
Superfamily Superfamily superfamily	c.7.1 — PFL-like glycyl radical enzymes
Family Family family	c.7.1.0 — automated matches

Domain ID domain_id	d6nd3f_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.7 — PFL-like glycyl radical enzymes
Superfamily Superfamily superfamily	c.7.1 — PFL-like glycyl radical enzymes
Family Family family	c.7.1.0 — automated matches

Domain ID domain_id	d6nd3g_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.7 — PFL-like glycyl radical enzymes
Superfamily Superfamily superfamily	c.7.1 — PFL-like glycyl radical enzymes
Family Family family	c.7.1.0 — automated matches

Domain ID domain_id	d6nd3h_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.7 — PFL-like glycyl radical enzymes
Superfamily Superfamily superfamily	c.7.1 — PFL-like glycyl radical enzymes
Family Family family	c.7.1.0 — automated matches

CATH v4.4 (8 domains)

Domain ID domain_id	6nd3A01
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	70 — Anaerobic Ribonucleotide-triphosphate Reductase Large Chain
Homologous superfamily homologous superfamily	20 —

Domain ID domain_id	6nd3B01
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	70 — Anaerobic Ribonucleotide-triphosphate Reductase Large Chain
Homologous superfamily homologous superfamily	20 —

Domain ID domain_id	6nd3C01
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	70 — Anaerobic Ribonucleotide-triphosphate Reductase Large Chain
Homologous superfamily homologous superfamily	20 —

Domain ID domain_id	6nd3D01
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	70 — Anaerobic Ribonucleotide-triphosphate Reductase Large Chain
Homologous superfamily homologous superfamily	20 —

Domain ID domain_id	6nd3E01
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	70 — Anaerobic Ribonucleotide-triphosphate Reductase Large Chain
Homologous superfamily homologous superfamily	20 —

Domain ID domain_id	6nd3F01
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	70 — Anaerobic Ribonucleotide-triphosphate Reductase Large Chain
Homologous superfamily homologous superfamily	20 —

Domain ID domain_id	6nd3G01
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	70 — Anaerobic Ribonucleotide-triphosphate Reductase Large Chain
Homologous superfamily homologous superfamily	20 —

Domain ID domain_id	6nd3H01
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	70 — Anaerobic Ribonucleotide-triphosphate Reductase Large Chain
Homologous superfamily homologous superfamily	20 —

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Unit-cell length a length_a	105.218 Å
Unit-cell length b length_b	234.700 Å
Unit-cell length c length_c	159.020 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	109.04 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	16

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

Resolution resolution	2.364 Å
Low-resolution limit resolution_low	49.730 Å
R factor r_factor	0.1867
R_work r_work	0.1858
R_free r_free	0.2157

wild-type choline TMA lyase in complex with betaine aldehyde

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

Choline trimethylamine-lyase

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

6nd3__assembly_4__model_1

6nd3__assembly_4__model_1 | I(q)

6nd3__assembly_4__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) 16 domains

SCOP 2.08 (8 domains)

CATH v4.4 (8 domains)

7. Citations (1)

wild-type choline TMA lyase in complex with betaine aldehyde

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

Choline trimethylamine-lyase

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

6nd3__assembly_4__model_1

6nd3__assembly_4__model_1 | I(q)

6nd3__assembly_4__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) 16 domains

SCOP 2.08 (8 domains)

CATH v4.4 (8 domains)

7. Citations (1)