SAXSdb — 2zxh

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

tRNA uridine 5-carboxymethylaminomethyl modification enzyme mnmG

Aquifex aeolicus

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	FLAVIN-ADENINE DINUCLEOTIDE × 2 PHOSPHATE ION × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	MNMG_AQUAE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 21–637； UniProt 1–617 Author chain B； PDBConstruct 21–637； UniProt 1–617

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	2zxh
Deposition date deposition_date	2008-12-24
Structure title title	Structure of Aquifex aeolicus GidA in the form I crystal
Keywords keywords	5-carboxymethylaminomethyluridine, modification, tRNA, wobble uridine, FAD, FAD-BINDING PROTEIN, tRNA modification enzyme; FAD-BINDING PROTEIN
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.

2zxh__assembly_1__model_1

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

Download this curve (.dat)

2zxh__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2zxh__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	32.94 Å
Rg (electron density)	32.18 Å
Total Rg	32.78 Å
Atom count	9714
Residues	1204
Excluded volume	173990 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2zxh__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 (3)

Entity 1 Entity 1 polymer

Description description	tRNA uridine 5-carboxymethylaminomethyl modification enzyme mnmG
Molecular weight formula_weight	71824.3 kDa
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	9714

MGSSHHHHHHSSGLVPAGSHMAWVVDEFDVVVIGGGHAGIEAALAAARMGAKTAMFVLNADTIGQMSCNPAIGGIAKGIVVREIDALGGEMGKAIDQTGIQFKMLNTRKGKAVQSPRAQADKKRYREYMKKVCENQENLYIKQEEVVDIIVKNNQVVGVRTNLGVEYKTKAVVVTTGTFLNGVIYIGDKMIPGGRLGEPRSEGLSDFYRRFDFPLIRFKTGTPARLDKRTIDFSALEVAPGDDPPPKFSFWTEPVGSYWFPKGKEQVNCWITYTTPKTHEIIRKNLHRTALYGGLIKGIGPRYCPSIEDKIVKFPDKERHQIFLEPEGLDTIEIYPNGLSTSLPEEVQWEMYRSIPGLENVVLIRPAYAIEYDVVPPTELYPTLETKKIRGLFHAGNFNGTTGYEEAAGQGIVAGINAALRAFGKEPIYLRRDESYIGVMIDDLTTKGVTEPYRLFTSRSEYRLYIRQDNAILRLAKLGRELGLLSEEQYKLVKELEREIEKWKEFYKSERVSVAVGGDTRSYSVATLMTMNYTLDDVKEKFGYEVPQHPYVKEEVEIQLKYEPYIERERKLNEKLKKLEDTKIPPDIDYDKIPGLTKEAREKLKKFKPITVGQASRIDGITPAAITALLVYLGKLD

Source Source

Source organism organism	Aquifex aeolicus
NCBI taxonomy ID ncbi_taxonomy_id	63363
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 non-polymer

Description description	FLAVIN-ADENINE DINUCLEOTIDE
Molecular weight formula_weight	785.5 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 non-polymer

Description description	PHOSPHATE ION
Molecular weight formula_weight	95.0 kDa
Source method src_method	syn
Copy count entity_count	3

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6. Fold Classification (SCOP + CATH) 6 domains

CATH v4.4 (6 domains)

Domain ID domain_id	2zxhA02
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	30 — Elongation Factor Tu (Ef-tu); domain 3
Homologous superfamily homologous superfamily	260 —

Domain ID domain_id	2zxhA03
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily	1800 — tRNA uridine 5-carboxymethylaminomethyl modification enzyme MnmG/GidA

Domain ID domain_id	2zxhA04
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	150 — DNA polymerase; domain 1
Homologous superfamily homologous superfamily	570 — GidA associated domain, C-terminal subdomain

Domain ID domain_id	2zxhB02
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	30 — Elongation Factor Tu (Ef-tu); domain 3
Homologous superfamily homologous superfamily	260 —

Domain ID domain_id	2zxhB03
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily	1800 — tRNA uridine 5-carboxymethylaminomethyl modification enzyme MnmG/GidA

Domain ID domain_id	2zxhB04
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	150 — DNA polymerase; domain 1
Homologous superfamily homologous superfamily	570 — GidA associated domain, C-terminal subdomain

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Unit-cell length a length_a	101.638 Å
Unit-cell length b length_b	213.272 Å
Unit-cell length c length_c	231.737 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	I 21 21 21
Space-group number int_tables_number	24
Crystal system crystal_system	—

Resolution resolution	3.200 Å
Low-resolution limit resolution_low	19.970 Å
R factor r_factor	0.2420
R_work r_work	0.2420
R_free r_free	0.2710

Structure of Aquifex aeolicus GidA in the form I crystal

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

tRNA uridine 5-carboxymethylaminomethyl modification enzyme mnmG

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

2zxh__assembly_1__model_1

2zxh__assembly_1__model_1 | I(q)

2zxh__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

6. Fold Classification (SCOP + CATH) 6 domains

CATH v4.4 (6 domains)

7. Citations (1)

Structure of Aquifex aeolicus GidA in the form I crystal

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

tRNA uridine 5-carboxymethylaminomethyl modification enzyme mnmG

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

2zxh__assembly_1__model_1

2zxh__assembly_1__model_1 | I(q)

2zxh__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

6. Fold Classification (SCOP + CATH) 6 domains

CATH v4.4 (6 domains)

7. Citations (1)