1x6m

Crystal structure of the glutathione-dependent formaldehyde-activating enzyme (Gfa)

Method: X-RAY DIFFRACTION

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

Glutathione-dependent formaldehyde-activating enzyme

Paracoccus denitrificans

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	ZINC ION × 4 SULFATE ION × 4 GLYCEROL × 1 water × 2	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 2	ZINC ION × 4 SULFATE ION × 3 GLYCEROL × 4 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	GFA_PARDE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 4–196； UniProt 1–193 Author chain B； PDBConstruct 4–196； UniProt 1–193 Author chain C； PDBConstruct 4–196； UniProt 1–193 Author chain D； PDBConstruct 4–196； UniProt 1–193

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	1x6m
Deposition date deposition_date	2004-08-11
Structure title title	Crystal structure of the glutathione-dependent formaldehyde-activating enzyme (Gfa)
Keywords keywords	zn-enzyme, formaldehyde, 3_10 helix, LYASE; 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.

1x6m__assembly_1__model_1

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

Download this curve (.dat)

1x6m__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1x6m__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	24.67 Å
Rg (electron density)	23.66 Å
Total Rg	24.44 Å
Atom count	2982
Residues	390
Excluded volume	52416 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1x6m__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`1x6m__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 (5)

Entity 1 Entity 1 polymer

Description description	Glutathione-dependent formaldehyde-activating enzyme
Molecular weight formula_weight	21191.1 kDa
EC 编号 ec_number	4.4.-.-
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	6262

GHMVDTSGVKIHPAVDNGIKPAQPGFAGGTLHCKCSTNPVRVAVRAQTAHNHVCGCTKCWKPEGAIFSQVAVVGRDALEVLEGAEKLEIVNAEAPIQRHRCRDCGVHMYGRIENRDHPFYGLDFVHTELSDEDGWSAPEFAAFVSSIIESGVDPSRMEAIRARLRELGLEPYDALSPPLMDAIATHIAKRSGALAA

Source Source

Source organism organism	Paracoccus denitrificans
NCBI taxonomy ID ncbi_taxonomy_id	266
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	8

Entity 3 Entity 3 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	7

Entity 4 Entity 4 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	5

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	255

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6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (8 domains)

Domain ID domain_id	d1x6ma1
Class class	b — All beta proteins
Fold Fold fold	b.88 — Mss4-like
Superfamily Superfamily superfamily	b.88.1 — Mss4-like
Family Family family	b.88.1.4 — Glutathione-dependent formaldehyde-activating enzyme, Gfa

Domain ID domain_id	d1x6ma2
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	d1x6mb1
Class class	b — All beta proteins
Fold Fold fold	b.88 — Mss4-like
Superfamily Superfamily superfamily	b.88.1 — Mss4-like
Family Family family	b.88.1.4 — Glutathione-dependent formaldehyde-activating enzyme, Gfa

Domain ID domain_id	d1x6mb2
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	d1x6mc1
Class class	b — All beta proteins
Fold Fold fold	b.88 — Mss4-like
Superfamily Superfamily superfamily	b.88.1 — Mss4-like
Family Family family	b.88.1.4 — Glutathione-dependent formaldehyde-activating enzyme, Gfa

Domain ID domain_id	d1x6mc2
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	d1x6md1
Class class	b — All beta proteins
Fold Fold fold	b.88 — Mss4-like
Superfamily Superfamily superfamily	b.88.1 — Mss4-like
Family Family family	b.88.1.4 — Glutathione-dependent formaldehyde-activating enzyme, Gfa

Domain ID domain_id	d1x6md2
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	1x6mA00
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	1590 — glutathione-dependent formaldehyde- activating enzyme (gfa)
Homologous superfamily homologous superfamily	10 — glutathione-dependent formaldehyde- activating enzyme (gfa)

Domain ID domain_id	1x6mB00
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	1590 — glutathione-dependent formaldehyde- activating enzyme (gfa)
Homologous superfamily homologous superfamily	10 — glutathione-dependent formaldehyde- activating enzyme (gfa)

Domain ID domain_id	1x6mC00
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	1590 — glutathione-dependent formaldehyde- activating enzyme (gfa)
Homologous superfamily homologous superfamily	10 — glutathione-dependent formaldehyde- activating enzyme (gfa)

Domain ID domain_id	1x6mD00
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	1590 — glutathione-dependent formaldehyde- activating enzyme (gfa)
Homologous superfamily homologous superfamily	10 — glutathione-dependent formaldehyde- activating enzyme (gfa)

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Unit-cell length a length_a	53.360 Å
Unit-cell length b length_b	118.860 Å
Unit-cell length c length_c	95.990 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	97.48 °
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	2.350 Å
Low-resolution limit resolution_low	74.290 Å
R factor r_factor	0.1935
R_work r_work	0.1892
R_free r_free	0.2502

Crystal structure of the glutathione-dependent formaldehyde-activating enzyme (Gfa)

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

Glutathione-dependent formaldehyde-activating enzyme

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

1x6m__assembly_1__model_1

1x6m__assembly_1__model_1 | I(q)

1x6m__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) 12 domains

SCOP 2.08 (8 domains)

CATH v4.4 (4 domains)

7. Citations (2)

Crystal structure of the glutathione-dependent formaldehyde-activating enzyme (Gfa)

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

Glutathione-dependent formaldehyde-activating enzyme

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

1x6m__assembly_1__model_1

1x6m__assembly_1__model_1 | I(q)

1x6m__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) 12 domains

SCOP 2.08 (8 domains)

CATH v4.4 (4 domains)

7. Citations (2)