SAXSdb — 2phn

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

F420-0:gamma-glutamyl ligase

Archaeoglobus fulgidus DSM 4304

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	MANGANESE (II) ION × 4 ACETATE ION × 4 GUANOSINE-5'-DIPHOSPHATE × 2 1,2-ETHANEDIOL × 4 GLYCEROL × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	COFE_ARCFU
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 4–252； UniProt 1–249 Author chain B； PDBConstruct 4–252； UniProt 1–249

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	2phn
Deposition date deposition_date	2007-04-11
Structure title title	Crystal structure of an amide bond forming F420-gamma glutamyl ligase from Archaeoglobus fulgidus
Keywords keywords	;gamma-glutamyl ligase, coenzyme F420 biosynthesis, amide bond forming enzyme, metal dependent, new fold, GDP binding, MCSG, Structural Genomics, PSI-2, Protein Structure Initiative, Midwest Center for Structural Genomics, LIGASE ;; LIGASE
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.

2phn__assembly_1__model_1

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

Download this curve (.dat)

2phn__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2phn__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	23.69 Å
Rg (electron density)	22.64 Å
Total Rg	23.35 Å
Atom count	3907
Residues	497
Excluded volume	69706 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2phn__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 (7)

Entity 1 Entity 1 polymer

Description description	F420-0:gamma-glutamyl ligase
Molecular weight formula_weight	27762.9 kDa
EC 编号 ec_number	6.3.2.-
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	4756

QGHMRVEVFPVEGLPLIKEGDDLAELISSRVRFEDGDVLVVCSTVISKAEGRIRRLEEFNPSERAKEIAARIGKPAEFVQAVLEESEEVLLDFPFLLVKAKFGNVCVNAGIDASNVEEGSLLLPPLDPDGSAEKLRRRILELTGKRVGVIITDTNGRCFRRGVVGFAIGISGVKAMKDWIGRKDLYGRELEVTVECVADEIAAFANLLMGEGGDGIPAVVVRGLNVAGEGSMEEIYRSEEEDVIRRCLKRCLGS

Source Source

Source organism organism	Archaeoglobus fulgidus DSM 4304
NCBI taxonomy ID ncbi_taxonomy_id	224325
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	MANGANESE (II) ION
Molecular weight formula_weight	54.9 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 3 Entity 3 non-polymer

Description description	ACETATE ION
Molecular weight formula_weight	59.0 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 4 Entity 4 non-polymer

Description description	GUANOSINE-5'-DIPHOSPHATE
Molecular weight formula_weight	443.2 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 non-polymer

Description description	1,2-ETHANEDIOL
Molecular weight formula_weight	62.1 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 6 Entity 6 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 7 Entity 7 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	576

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6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d2phna_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.340 — CofE-like
Superfamily Superfamily superfamily	d.340.1 — CofE-like
Family Family family	d.340.1.1 — CofE-like

Domain ID domain_id	d2phnb_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.340 — CofE-like
Superfamily Superfamily superfamily	d.340.1 — CofE-like
Family Family family	d.340.1.1 — CofE-like

CATH v4.4 (4 domains)

Domain ID domain_id	2phnA01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1330 — 60s Ribosomal Protein L30; Chain: A;
Homologous superfamily homologous superfamily	100 — CofE-like

Domain ID domain_id	2phnA02
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	1660 — CofE-like fold
Homologous superfamily homologous superfamily	10 — CofE-like domain

Domain ID domain_id	2phnB01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1330 — 60s Ribosomal Protein L30; Chain: A;
Homologous superfamily homologous superfamily	100 — CofE-like

Domain ID domain_id	2phnB02
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	1660 — CofE-like fold
Homologous superfamily homologous superfamily	10 — CofE-like domain

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Unit-cell length a length_a	98.367 Å
Unit-cell length b length_b	98.367 Å
Unit-cell length c length_c	94.347 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	16

Space group space_group	P 41 21 2
Space-group number int_tables_number	92
Crystal system crystal_system	—

Resolution resolution	1.350 Å
Low-resolution limit resolution_low	40.000 Å
R factor r_factor	0.1618
R_work r_work	0.1603
R_free r_free	0.1900

Crystal structure of an amide bond forming F420-gamma glutamyl ligase from Archaeoglobus fulgidus

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

F420-0:gamma-glutamyl ligase

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

2phn__assembly_1__model_1

2phn__assembly_1__model_1 | I(q)

2phn__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 (7)

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 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 water

6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (2 domains)

CATH v4.4 (4 domains)

7. Citations (1)

Crystal structure of an amide bond forming F420-gamma glutamyl ligase from Archaeoglobus fulgidus

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

F420-0:gamma-glutamyl ligase

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

2phn__assembly_1__model_1

2phn__assembly_1__model_1 | I(q)

2phn__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 (7)

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 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 water

6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (2 domains)

CATH v4.4 (4 domains)

7. Citations (1)