SAXSdb — 2y4k

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

MANNOSYLGLYCERATE SYNTHASE

RHODOTHERMUS MARINUS

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	MAGNESIUM ION × 1 GUANOSINE-5'-DIPHOSPHATE × 1 CHLORIDE ION × 1 FORMIC ACID × 3 water × 1	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	MAGNESIUM ION × 1 GUANOSINE-5'-DIPHOSPHATE × 1 CHLORIDE ION × 1 FORMIC ACID × 3 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q9RFR0_RHOMR
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–382； UniProt 1–382 Author chain B； PDBConstruct 1–382； UniProt 1–382

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	2y4k
Deposition date deposition_date	2011-01-07
Structure title title	MANNOSYLGLYCERATE SYNTHASE IN COMPLEX WITH MG-GDP
Keywords keywords	TRANSFERASE, GLYCOSYLTRANSFERASE; 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.

2y4k__assembly_1__model_1

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

Download this curve (.dat)

2y4k__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2y4k__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	21.90 Å
Rg (electron density)	20.91 Å
Total Rg	21.72 Å
Atom count	3110
Residues	380
Excluded volume	54906 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2y4k__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`2y4k__assembly_2__model_1`	monomeric （1）	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 (7)

Entity 1 Entity 1 polymer

Description description	MANNOSYLGLYCERATE SYNTHASE
Molecular weight formula_weight	44600.7 kDa
EC 编号 ec_number	2.4.1.217
Mutation mutation	YES
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	6449

MSLVVFPFKHEHPEVLLHNVRVAAAHPRVHEVLCIGYERDQTYEAVERAAPEISRATGTPVSVRLQERLGTLRPGKGDGMNTALRYFLEETQWERIHFYDADITSFGPDWITKAEEAADFGYGLVRHYFPRASTDAMITWMITRTGFALLWPHTELSWIEQPLGGELLMRREVAAMLYEDERVRRRSDWGIDTLYTFVTVAAGVSIYECYIPEGKAHRLYGGLDDLRTMLVECFAAIQSLQHEVVGQPAIHRQEHPHRVPVHIAERVGYDVEATLHRLMQHWTPRQVELLELFTTPVREGLRTCQRRPAFNFMDEMAWAATYHVLLEHFQPGDPDWEELLFKLWTTRVLNYTMTVALRGYDYAQQYLYRMLGRYRYQAALEN

Source Source

Source organism organism	RHODOTHERMUS MARINUS
NCBI taxonomy ID ncbi_taxonomy_id	518766
Host organism host_organism	ESCHERICHIA COLI

Entity 2 Entity 2 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 non-polymer

Description description	GUANOSINE-5'-DIPHOSPHATE
Molecular weight formula_weight	443.2 kDa
Source method src_method	syn
Copy count entity_count	2

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	2

Entity 5 Entity 5 non-polymer

Description description	FORMIC ACID
Molecular weight formula_weight	46.0 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 6 Entity 6 non-polymer

Description description	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
Molecular weight formula_weight	122.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 7 Entity 7 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	145

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6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d2y4ka_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.68 — Nucleotide-diphospho-sugar transferases
Superfamily Superfamily superfamily	c.68.1 — Nucleotide-diphospho-sugar transferases
Family Family family	c.68.1.18 — MGS-like

Domain ID domain_id	d2y4kb_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.68 — Nucleotide-diphospho-sugar transferases
Superfamily Superfamily superfamily	c.68.1 — Nucleotide-diphospho-sugar transferases
Family Family family	c.68.1.18 — MGS-like

CATH v4.4 (2 domains)

Domain ID domain_id	2y4kA01
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	550 — Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A
Homologous superfamily homologous superfamily	10 — Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A

Domain ID domain_id	2y4kB01
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	550 — Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A
Homologous superfamily homologous superfamily	10 — Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A

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Unit-cell length a length_a	149.646 Å
Unit-cell length b length_b	149.646 Å
Unit-cell length c length_c	154.112 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 32 2 1
Space-group number int_tables_number	154
Crystal system crystal_system	—

Resolution resolution	2.450 Å
Low-resolution limit resolution_low	47.760 Å
R factor r_factor	0.2021
R_work r_work	0.2009
R_free r_free	0.2248

MANNOSYLGLYCERATE SYNTHASE IN COMPLEX WITH MG-GDP

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

MANNOSYLGLYCERATE SYNTHASE

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

2y4k__assembly_1__model_1

2y4k__assembly_1__model_1 | I(q)

2y4k__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 (7)

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 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 water

6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)

MANNOSYLGLYCERATE SYNTHASE IN COMPLEX WITH MG-GDP

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

MANNOSYLGLYCERATE SYNTHASE

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

2y4k__assembly_1__model_1

2y4k__assembly_1__model_1 | I(q)

2y4k__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 (7)

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 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 water

6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)