SAXSdb — 6ygl

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

Queuine tRNA-ribosyltransferase

Zymomonas mobilis subsp. mobilis (strain ATCC 31821 / ZM4 / CP4)

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	GLYCEROL × 4 ZINC ION × 2 CHLORIDE ION × 2 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	TGT_ZYMMO
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 3–388； UniProt 1–386

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	6ygl
Deposition date deposition_date	2020-03-27
Structure title title	TGT W326F mutant labelled mit 5F-Trp crystallised at pH 5.5
Keywords keywords	TRANSFERASE, TGT, TRNA-GUANINE TRANSGLYCOSYLASE, GUANINE INSERTION ENZYME, HOMODIMER, 19F-NMR, 5F-TRP; TRANSFERASE
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.

6ygl__assembly_1__model_1

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

Download this curve (.dat)

6ygl__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

6ygl__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	30.93 Å
Rg (electron density)	30.27 Å
Total Rg	30.68 Å
Atom count	10938
Residues	724
Excluded volume	98891 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`6ygl__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 (5)

Entity 1 Entity 1 polymer

Description description	Queuine tRNA-ribosyltransferase
Molecular weight formula_weight	43084.8 kDa
EC 编号 ec_number	2.4.2.29
Mutation mutation	T312K
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	5979

GSMVEATAQETDRPRFSFSIAAREGKARTGTIEMKRGVIRTPAFMPVGTAATVKALKPETVRATGADIILGNTYHLMLRPGAERIAKLGGLHSFMGWDRPILTDSGGYQVMSLSSLTKQSEEGVTFKSHLDGSRHMLSPERSIEIQHLLGSDIVMAFDECTPYPATPSRAASSMERSMRWAKRSRDAFDSRKEQAENAALFGIQQGSVFENLRQQSADALAEIGFDGYAVGGLAVGEGQDEMFRVLDFSVPMLPDDKPHYLMGVGKPDDIVGAVERGIDMFDCVLPTRSGRNGQAFTWDGPINIRNARFSEDLKPLDSECHCAVCQKFSRAYIHHLIRAGEILGAMLMTEHNIAFYQQLMQKIRDSISEGRFSQFAQDFRARYFARNS

Source Source

Source organism organism	Zymomonas mobilis subsp. mobilis (strain ATCC 31821 / ZM4 / CP4)
NCBI taxonomy ID ncbi_taxonomy_id	264203
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	351

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6. Fold Classification (SCOP + CATH) 1 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d6ygla_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamily	c.1.20 — tRNA-guanine transglycosylase
Family Family family	c.1.20.1 — tRNA-guanine transglycosylase

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Unit-cell length a length_a	91.130 Å
Unit-cell length b length_b	65.204 Å
Unit-cell length c length_c	70.673 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	96.10 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	monoclinic

Resolution resolution	1.480 Å
Low-resolution limit resolution_low	45.310 Å
R factor r_factor	0.1340
R_work r_work	0.1324
R_free r_free	0.1640

TGT W326F mutant labelled mit 5F-Trp crystallised at pH 5.5

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

Queuine tRNA-ribosyltransferase

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

6ygl__assembly_1__model_1

6ygl__assembly_1__model_1 | I(q)

6ygl__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 (5)

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 water

6. Fold Classification (SCOP + CATH) 1 domains

SCOP 2.08 (1 domains)

7. Citations (1)

TGT W326F mutant labelled mit 5F-Trp crystallised at pH 5.5

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

Queuine tRNA-ribosyltransferase

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

6ygl__assembly_1__model_1

6ygl__assembly_1__model_1 | I(q)

6ygl__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 (5)

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 water

6. Fold Classification (SCOP + CATH) 1 domains

SCOP 2.08 (1 domains)

7. Citations (1)