SAXSdb — 3c8n

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

Probable F420-dependent glucose-6-phosphate dehydrogenase FGD1

Mycobacterium tuberculosis

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	water × 2	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 2	water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	P96253_MYCTU
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 21–356； UniProt 1–336 Author chain B； PDBConstruct 21–356； UniProt 1–336 Author chain C； PDBConstruct 21–356； UniProt 1–336 Author chain D； PDBConstruct 21–356； UniProt 1–336

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	3c8n
Deposition date deposition_date	2008-02-12
Structure title title	Crystal structure of apo-FGD1 from Mycobacterium tuberculosis
Keywords keywords	TIM barrel, non-prolyl cis-peptide, 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.

3c8n__assembly_1__model_1

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

Download this curve (.dat)

3c8n__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3c8n__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	26.93 Å
Rg (electron density)	25.97 Å
Total Rg	26.74 Å
Atom count	5226
Residues	657
Excluded volume	92553 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3c8n__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`3c8n__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 (2)

Entity 1 Entity 1 polymer

Description description	Probable F420-dependent glucose-6-phosphate dehydrogenase FGD1
Molecular weight formula_weight	39690.1 kDa
EC 编号 ec_number	1.-.-.-
Mutation mutation	L243M
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	10741

MGSSHHHHHHSSGLVPRGSHMAELKLGYKASAEQFAPRELVELAVAAEAHGMDSATVSDHFQPWRHQGGHAPFSLSWMTAVGERTNRLLLGTSVLTPTFRYNPAVIAQAFATMGCLYPNRVFLGVGTGEALNEIATGYEGAWPEFKERFARLRESVGLMRQLWSGDRVDFDGDYYRLKGASIYDVPDGGVPVYIAAGGPAVAKYAGRAGDGFICTSGKGEELYTEKLMPAVREGAAAADRSVDGIDKMIEIKISYDPDPELAMNNTRFWAPLSLTAEQKHSIDDPIEMEKAADALPIEQIAKRWIVASDPDEAVEKVGQYVTWGLNHLVFHAPGHDQRRFLELFQSDLAPRLRRLG

Source Source

Source organism organism	Mycobacterium tuberculosis
NCBI taxonomy ID ncbi_taxonomy_id	83332
Host organism host_organism	Mycobacterium smegmatis

Entity 2 Entity 2 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	371

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6. Fold Classification (SCOP + CATH) 9 domains

SCOP 2.08 (5 domains)

Domain ID domain_id	d3c8na1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamily	c.1.16 — Bacterial luciferase-like
Family Family family	c.1.16.0 — automated matches

Domain ID domain_id	d3c8na2
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	d3c8nb_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamily	c.1.16 — Bacterial luciferase-like
Family Family family	c.1.16.0 — automated matches

Domain ID domain_id	d3c8nc_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamily	c.1.16 — Bacterial luciferase-like
Family Family family	c.1.16.0 — automated matches

Domain ID domain_id	d3c8nd_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamily	c.1.16 — Bacterial luciferase-like
Family Family family	c.1.16.0 — automated matches

CATH v4.4 (4 domains)

Domain ID domain_id	3c8nA00
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	20 — TIM Barrel
Homologous superfamily homologous superfamily	30 — Luciferase-like domain

Domain ID domain_id	3c8nB00
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	20 — TIM Barrel
Homologous superfamily homologous superfamily	30 — Luciferase-like domain

Domain ID domain_id	3c8nC00
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	20 — TIM Barrel
Homologous superfamily homologous superfamily	30 — Luciferase-like domain

Domain ID domain_id	3c8nD00
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	20 — TIM Barrel
Homologous superfamily homologous superfamily	30 — Luciferase-like domain

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Unit-cell length a length_a	80.954 Å
Unit-cell length b length_b	89.133 Å
Unit-cell length c length_c	90.859 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	91.64 °
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	1.900 Å
Low-resolution limit resolution_low	40.100 Å
R factor r_factor	0.2140
R_work r_work	0.2120
R_free r_free	0.2550

Crystal structure of apo-FGD1 from Mycobacterium tuberculosis

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

Probable F420-dependent glucose-6-phosphate dehydrogenase FGD1

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

3c8n__assembly_1__model_1

3c8n__assembly_1__model_1 | I(q)

3c8n__assembly_1__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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 water

6. Fold Classification (SCOP + CATH) 9 domains

SCOP 2.08 (5 domains)

CATH v4.4 (4 domains)

7. Citations (1)

Crystal structure of apo-FGD1 from Mycobacterium tuberculosis

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

Probable F420-dependent glucose-6-phosphate dehydrogenase FGD1

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

3c8n__assembly_1__model_1

3c8n__assembly_1__model_1 | I(q)

3c8n__assembly_1__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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 water

6. Fold Classification (SCOP + CATH) 9 domains

SCOP 2.08 (5 domains)

CATH v4.4 (4 domains)

7. Citations (1)