SAXSdb — 3cp8

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

tRNA uridine 5-carboxymethylaminomethyl modification enzyme gidA

Chlorobium tepidum

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	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 2	FLAVIN-ADENINE DINUCLEOTIDE × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	GIDA_CHLTE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 21–641； UniProt 1–621 Author chain B； PDBConstruct 21–641； UniProt 1–621 Author chain C； PDBConstruct 21–641； UniProt 1–621 Author chain D； PDBConstruct 21–641； UniProt 1–621

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	3cp8
Deposition date deposition_date	2008-03-31
Structure title title	Crystal structure of GidA from Chlorobium tepidum
Keywords keywords	;Rossmann fold, FAD-binding domain, dinucleotide-binding motif, glutathione reductase, oxido-reductase, tRNA-modification, Cytoplasm, Flavoprotein, tRNA processing, 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.

3cp8__assembly_2__model_1

Assembly 2 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

3cp8__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3cp8__assembly_2__model_1 | P(r) · Pending

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

Rg（Guinier）	35.01 Å
Rg (electron density)	34.96 Å
Total Rg	35.47 Å
Atom count	9053
Residues	1163
Excluded volume	160700 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3cp8__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`3cp8__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	tRNA uridine 5-carboxymethylaminomethyl modification enzyme gidA
Molecular weight formula_weight	70357.2 kDa
EC 编号 ec_number	1.-.-.-
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	18567

MGSSHHHHHHSSGLVPRGSHMYDVIVVGAGHAGCEAALAVARGGLHCLLITSDLSAVARMSCNPAIGGVAKGQITREIDALGGEMGKAIDATGIQFRMLNRSKGPAMHSPRAQADKTQYSLYMRRIVEHEPNIDLLQDTVIGVSANSGKFSSVTVRSGRAIQAKAAILACGTFLNGLIHIGMDHFPGGRSTAEPPVEGLTESLASLGFSFGRLKTGTPPRIDSRSVDYTIVTEQPGDVDPVPFSFSSTSVANRNLVSCYLTKTTEKTHDILRTGFDRSPLFTGKVQGVGPRYCPSIEDKISRFPDKSSHHIFLEPEGTDTVEMYVNGFSTSLPEDIQIAGLRSIPGLEEAKMIRPGYAIEYDFFHPWQIRSTMETRPVENLFFAGQINGTSGYEEAAAQGLMAGINAVRKILGKELIVLGRDQAYIGVLIDDLITKETKEPYRMFTSSAEHRLILRHDNADLRLRKIGYDCNLVSSDDLHRTESIIKRVQHCLEVMKTAKVTPAEINTLLMNKGLQELKTPARALSLIKRPGISLQDILEHSLSVRSAAEELCNDPRVAEQVQIEIKYEGYIKREQLVADRIARLDSLHIPDNFNYDSLNSLSSEGREKLLKHRPATIGQASRILGVSPSDVSILMIRLGR

Source Source

Source organism organism	Chlorobium tepidum
Host organism host_organism	Escherichia coli

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	4

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6. Fold Classification (SCOP + CATH) 11 domains

CATH v4.4 (11 domains)

Domain ID domain_id	3cp8A02
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	3cp8A03
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	3cp8A04
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	3cp8B02
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	3cp8B03
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	3cp8B04
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	3cp8C02
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	3cp8C03
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	3cp8C04
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	3cp8D02
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	3cp8D03
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	120.505 Å
Unit-cell length b length_b	71.836 Å
Unit-cell length c length_c	171.934 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	91.82 °
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	3.200 Å
Low-resolution limit resolution_low	44.850 Å
R factor r_factor	0.2557
R_work r_work	0.2544
R_free r_free	0.2781

Crystal structure of GidA from Chlorobium tepidum

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

3cp8__assembly_2__model_1

3cp8__assembly_2__model_1 | I(q)

3cp8__assembly_2__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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

6. Fold Classification (SCOP + CATH) 11 domains

CATH v4.4 (11 domains)

7. Citations (1)

Crystal structure of GidA from Chlorobium tepidum

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

3cp8__assembly_2__model_1

3cp8__assembly_2__model_1 | I(q)

3cp8__assembly_2__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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

6. Fold Classification (SCOP + CATH) 11 domains

CATH v4.4 (11 domains)

7. Citations (1)