SAXSdb — 3b4y

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

PROBABLE F420-DEPENDENT GLUCOSE-6-PHOSPHATE DEHYDROGENASE FGD1

Mycobacterium tuberculosis H37Rv

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	COENZYME F420 × 2 CITRATE ANION × 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

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	3b4y
Deposition date deposition_date	2007-10-25
Structure title title	FGD1 (Rv0407) from Mycobacterium tuberculosis
Keywords keywords	;TIM-barrel, non-prolyl cis-peptide bulge, F420 binding, Oxidoreductase, Structural Genomics, TB Structural Genomics Consortium, TBSGC ;; 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.

3b4y__assembly_1__model_1

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

Download this curve (.dat)

3b4y__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3b4y__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	26.74 Å
Rg (electron density)	25.88 Å
Total Rg	26.64 Å
Atom count	5254
Residues	646
Excluded volume	92782 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3b4y__assembly_1__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 (4)

Entity 1 Entity 1 polymer

Description description	PROBABLE F420-DEPENDENT GLUCOSE-6-PHOSPHATE DEHYDROGENASE FGD1
Molecular weight formula_weight	39706.1 kDa
EC 编号 ec_number	1.-.-.-
Mutation mutation	L243(MSE)
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	5474

MGSSHHHHHHSSGLVPRGSHMAELKLGYKASAEQFAPRELVELAVAAEAHGMDSATVSDHFQPWRHQGGHAPFSLSWMTAVGERTNRLLLGTSVLTPTFRYNPAVIAQAFATMGCLYPNRVFLGVGTGEALNEIATGYEGAWPEFKERFARLRESVGLMRQLWSGDRVDFDGDYYRLKGASIYDVPDGGVPVYIAAGGPAVAKYAGRAGDGFICTSGKGEELYTEKLMPAVREGAAAADRSVDGIDKMIEIKISYDPDPELAMNNTRFWAPLSLTAEQKHSIDDPIEMEKAADALPIEQIAKRWIVASDPDEAVEKVGQYVTWGLNHLVFHAPGHDQRRFLELFQSDLAPRLRRLG

Source Source

Source organism organism	Mycobacterium tuberculosis H37Rv
NCBI taxonomy ID ncbi_taxonomy_id	83332
Host organism host_organism	Mycobacterium smegmatis

Entity 2 Entity 2 non-polymer

Description description	COENZYME F420
Molecular weight formula_weight	773.6 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 non-polymer

Description description	CITRATE ANION
Molecular weight formula_weight	189.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	195

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6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d3b4ya_
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	d3b4yb_
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 (2 domains)

Domain ID domain_id	3b4yA00
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	3b4yB00
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	91.078 Å
Unit-cell length b length_b	89.907 Å
Unit-cell length c length_c	80.146 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	P 21 21 2
Space-group number int_tables_number	18
Crystal system crystal_system	—

Resolution resolution	1.950 Å
Low-resolution limit resolution_low	24.650 Å
R factor r_factor	0.1938
R_work r_work	0.1917
R_free r_free	0.2343

FGD1 (Rv0407) 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

3b4y__assembly_1__model_1

3b4y__assembly_1__model_1 | I(q)

3b4y__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 (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) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)

FGD1 (Rv0407) 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

3b4y__assembly_1__model_1

3b4y__assembly_1__model_1 | I(q)

3b4y__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 (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) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)