SAXSdb — 3kia

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

Mannosyl-3-phosphoglycerate synthase

Rubrobacter xylanophilus

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	GUANOSINE-5'-MONOPHOSPHATE × 2 CHLORIDE ION × 3 MAGNESIUM ION × 3 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	B7SY86_9ACTN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 53–387； UniProt 1–335 Author chain C； PDBConstruct 53–387； UniProt 1–335

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	3kia
Deposition date deposition_date	2009-11-01
Structure title title	Crystal structure of mannosyl-3-phosphoglycerate synthase from Rubrobacter xylanophilus
Keywords keywords	;GT-A TYPE GLYCOSYLTRANSFERASE, GT-81, MANNOSYL-3-PHOSPHOGLYCERATE SYNTHASE, RUBROBACTER XYLANOPHILUS, GDP-MANNOSE, 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.

3kia__assembly_1__model_1

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

Download this curve (.dat)

3kia__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3kia__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	27.51 Å
Rg (electron density)	26.59 Å
Total Rg	27.29 Å
Atom count	4909
Residues	621
Excluded volume	86790 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3kia__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	Mannosyl-3-phosphoglycerate synthase
Molecular weight formula_weight	43047.4 kDa
EC 编号 ec_number	2.4.1.217
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,C
Atom count atom_count	5023

MHHHHHHSSGLVPRGSGMKETAAAKFERQHMDSPDLGTDDDDKAMADIGSEFMSTYHERPLGPASAAEWFRQRSYDYGQFPPEDLARRKRELGLTVSAVLPSRNVADTVGGIIDEIHALNERAPLIDQILVVDADSEDGTAGVAASHGAEVYSENELMSGYGDAHGKGDAMWRALSVTRGDLVLYIDADTRDFRPQLAYGVLGPVLEVPGVRFVKAAYRRPFRKGESIEEDGGGRVTELTAKPLFNLFYPELAGFVQPLAGEFVADRELFCSIPFLTGYAVETGIMIDVLKKVGLGAMAQVDLGERQNRHQHLRDLSRMSYAVVRAVARRLRQEGRLQQLREPGLPESFFQLSDYLHAVATPEGLKLQEYVEELVERPPINEVLRVR

Source Source

Source organism organism	Rubrobacter xylanophilus
NCBI taxonomy ID ncbi_taxonomy_id	49319
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	GUANOSINE-5'-MONOPHOSPHATE
Molecular weight formula_weight	363.2 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 4 Entity 4 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	106

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6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id	3kiaA00
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	3kiaC00
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	109.010 Å
Unit-cell length b length_b	109.010 Å
Unit-cell length c length_c	313.418 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	24

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

Resolution resolution	2.800 Å
Low-resolution limit resolution_low	53.699 Å
R factor r_factor	0.1924
R_work r_work	0.1899
R_free r_free	0.2392

Crystal structure of mannosyl-3-phosphoglycerate synthase from Rubrobacter xylanophilus

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

Mannosyl-3-phosphoglycerate 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

3kia__assembly_1__model_1

3kia__assembly_1__model_1 | I(q)

3kia__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) 2 domains

CATH v4.4 (2 domains)

7. Citations (1)

Crystal structure of mannosyl-3-phosphoglycerate synthase from Rubrobacter xylanophilus

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

Mannosyl-3-phosphoglycerate 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

3kia__assembly_1__model_1

3kia__assembly_1__model_1 | I(q)

3kia__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) 2 domains

CATH v4.4 (2 domains)

7. Citations (1)