SAXSdb — 3cp2

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

tRNA uridine 5-carboxymethylaminomethyl modification enzyme gidA

Escherichia coli

State in the Current Structure

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

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	GIDA_ECOLI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 21–649； UniProt 1–629

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	3cp2
Deposition date deposition_date	2008-03-30
Structure title title	Crystal structure of GidA from E. coli
Keywords keywords	FAD, NAD, oxidoreductase, tRNA, Cytoplasm, Flavoprotein, tRNA processing; 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.

3cp2__assembly_1__model_1

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

Download this curve (.dat)

3cp2__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3cp2__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	34.04 Å
Rg (electron density)	33.58 Å
Total Rg	33.98 Å
Atom count	7590
Residues	982
Excluded volume	134550 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3cp2__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 gidA
Molecular weight formula_weight	71774.5 kDa
EC 编号 ec_number	1.-.-.-
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	3800

MGSSHHHHHHSSGLVPRGSHMFYPDPFDVIIIGGGHAGTEAAMAAARMGQQTLLLTHNIDTLGQMSCNPAIGGIGKGHLVKEVDALGGLMAKAIDQAGIQFRILNASKGPAVRATRAQADRVLYRQAVRTALENQPNLMIFQQAVEDLIVENDRVVGAVTQMGLKFRAKAVVLTVGTFLDGKIHIGLDNYSGGRAGDPPSIPLSRRLRELPLRVGRLKTGTPPRIDARTIDFSVLAQQHGDNPMPVFSFMGNASQHPQQVPCYITHTNEKTHDVIRSNLDRSPMYAGVIEGVGPRYCPSIEDKVMRFADRNQHQIFLEPEGLTSNEIYPNGISTSLPFDVQMQIVRSMQGMENAKIVRPGYAIEYDFFDPRDLKPTLESKFIQGLFFAGQINGTTGYEEAAAQGLLAGLNAARLSADKEGWAPARSQAYLGVLVDDLCTLGTKEPYRMFTSRAEYRLMLREDNADLRLTEIGRELGLVDDERWARFNEKLENIERERQRLKSTWVTPSAEAAAEVNAHLTAPLSREASGEDLLRRPEMTYEKLTTLTPFAPALTDEQAAEQVEIQVKYEGYIARQQDEIEKQLRNENTLLPATLDYRQVSGLSNEVIAKLNDHKPASIGQASRISGVTPAAISILLVWLKKQGMLRRSA

Source Source

Source organism organism	Escherichia coli
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	5

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6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id	3cp2A02
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	3cp2A03
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

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Unit-cell length a length_a	197.600 Å
Unit-cell length b length_b	197.600 Å
Unit-cell length c length_c	69.160 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	12

Space group space_group	P 65 2 2
Space-group number int_tables_number	179
Crystal system crystal_system	—

Resolution resolution	2.900 Å
Low-resolution limit resolution_low	19.960 Å
R factor r_factor	0.2490
R_work r_work	0.2457
R_free r_free	0.3135

Crystal structure of GidA from E. coli

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

tRNA uridine 5-carboxymethylaminomethyl modification enzyme gidA

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

3cp2__assembly_1__model_1

3cp2__assembly_1__model_1 | I(q)

3cp2__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 water

6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

7. Citations (1)

Crystal structure of GidA from E. coli

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

tRNA uridine 5-carboxymethylaminomethyl modification enzyme gidA

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

3cp2__assembly_1__model_1

3cp2__assembly_1__model_1 | I(q)

3cp2__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 water

6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

7. Citations (1)