SAXSdb — 4rif

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

Glycosyl transferase homolog

Streptomyces cyanogenus

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	;2'-deoxy-5'-O-[(R)-{[(R)-{[(1S,3R,4R,5S)-3,4-dihydroxy-5-methylcyclohexyl]oxy}(hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]-3,4-dihydrothymidine ; × 2 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q9ZGC0_STRCY
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–373； UniProt 1–373 Author chain B； PDBConstruct 1–373； UniProt 1–373

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	4rif
Deposition date deposition_date	2014-10-06
Structure title title	Landomycin Glycosyltransferase LanGT2, carbasugar substrate complex
Keywords keywords	GT fold, glycosyltransferase, transferase; 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.

4rif__assembly_1__model_1

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

Download this curve (.dat)

4rif__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

4rif__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	27.99 Å
Rg (electron density)	26.69 Å
Total Rg	27.49 Å
Atom count	5671
Residues	749
Excluded volume	100970 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`4rif__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	Glycosyl transferase homolog
Molecular weight formula_weight	40406.1 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	5884

MKILFVASGSPATVFALAPLATAARNAGHDVFMGAVEDMVPYIASAGIPALSIAPSSIRRYATMDREGNPVRMPETPEEELDFAGHWFGRMAAGSMDALREVTANWRPDLVVGGSMSFAAALIAAELGVPYVRQAWDTGDAWRTDPAASDELRPELRALGLDRLPDPALFVDICPPSLRPATAPPAQMMRWVPANGQRRLEPWMYTKGNRPRILVTSGSRLVFAKKTGFLRGLVADMAALDAEVVIATLDEVAEELRTELPGVRAGWVPLDVVVPTCDVVVHHAGGVTALTAMNAGVPQLIVPQGGNFVEAGLRISDFGAAITVDENTPEAVEKACGELIGNPSYAERARELSAEIAALPLPAEVVGALEGLVENLYFQ

Source Source

Source organism organism	Streptomyces cyanogenus
NCBI taxonomy ID ncbi_taxonomy_id	80860
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	;2'-deoxy-5'-O-[(R)-{[(R)-{[(1S,3R,4R,5S)-3,4-dihydroxy-5-methylcyclohexyl]oxy}(hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]-3,4-dihydrothymidine ;
Molecular weight formula_weight	530.4 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	208

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6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d4rifa1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.87 — UDP-Glycosyltransferase/glycogen phosphorylase
Superfamily Superfamily superfamily	c.87.1 — UDP-Glycosyltransferase/glycogen phosphorylase
Family Family family	c.87.1.0 — automated matches

Domain ID domain_id	d4rifa2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d4rifb1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.87 — UDP-Glycosyltransferase/glycogen phosphorylase
Superfamily Superfamily superfamily	c.87.1 — UDP-Glycosyltransferase/glycogen phosphorylase
Family Family family	c.87.1.0 — automated matches

Domain ID domain_id	d4rifb2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

CATH v4.4 (4 domains)

Domain ID domain_id	4rifA01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	2000 — Glycogen Phosphorylase B;

Domain ID domain_id	4rifA02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	2000 — Glycogen Phosphorylase B;

Domain ID domain_id	4rifB01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	2000 — Glycogen Phosphorylase B;

Domain ID domain_id	4rifB02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	2000 — Glycogen Phosphorylase B;

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Unit-cell length a length_a	57.970 Å
Unit-cell length b length_b	59.710 Å
Unit-cell length c length_c	71.990 Å
Unit-cell angle α angle_alpha	87.30 °
Unit-cell angle β angle_beta	73.97 °
Unit-cell angle γ angle_gamma	64.92 °
Molecules per unit cell Z z_pdb	2

Space group space_group	P 1
Space-group number int_tables_number	1
Crystal system crystal_system	—

Resolution resolution	1.850 Å
Low-resolution limit resolution_low	50.360 Å
R factor r_factor	0.1769
R_work r_work	0.1758
R_free r_free	0.1982

Landomycin Glycosyltransferase LanGT2, carbasugar substrate complex

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

Glycosyl transferase homolog

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

4rif__assembly_1__model_1

4rif__assembly_1__model_1 | I(q)

4rif__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) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

7. Citations (1)

Landomycin Glycosyltransferase LanGT2, carbasugar substrate complex

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

Glycosyl transferase homolog

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

4rif__assembly_1__model_1

4rif__assembly_1__model_1 | I(q)

4rif__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) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

7. Citations (1)