SAXSdb — 3d8v

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

Bifunctional protein glmU

Mycobacterium tuberculosis

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 3	URIDINE-DIPHOSPHATE-N-ACETYLGLUCOSAMINE × 3 water × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	GLMU_MYCTU
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–495； UniProt 1–495

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	3d8v
Deposition date deposition_date	2008-05-25
Structure title title	Crystal structure of GlmU from Mycobacterium tuberculosis in complex with uridine-diphosphate-N-acetylglucosamine
Keywords keywords	;Nucleotide-diphospho-sugar transferases/Single-stranded left-handed beta-helix, Acyltransferase, Cell shape, Cell wall biogenesis/degradation, Cytoplasm, Magnesium, Metal-binding, Multifunctional enzyme, Nucleotidyltransferase, Peptidoglycan synthesis, 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.

3d8v__assembly_1__model_1

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

Download this curve (.dat)

3d8v__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3d8v__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	37.23 Å
Rg (electron density)	36.41 Å
Total Rg	36.75 Å
Atom count	10461
Residues	1434
Excluded volume	183980 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3d8v__assembly_1__model_1`	trimeric （3）	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	Bifunctional protein glmU
Molecular weight formula_weight	51637.7 kDa
EC 编号 ec_number	2.7.7.23, 2.3.1.157
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	3652

MTFPGDTAVLVLAAGPGTRMRSDTPKVLHTLAGRSMLSHVLHAIAKLAPQRLIVVLGHDHQRIAPLVGELADTLGRTIDVALQDRPLGTGHAVLCGLSALPDDYAGNVVVTSGDTPLLDADTLADLIATHRAVSAAVTVLTTTLDDPFGYGRILRTQDHEVMAIVEQTDATPSQREIREVNAGVYAFDIAALRSALSRLSSNNAQQELYLTDVIAILRSDGQTVHASHVDDSALVAGVNNRVQLAELASELNRRVVAAHQLAGVTVVDPATTWIDVDVTIGRDTVIHPGTQLLGRTQIGGRCVVGPDTTLTDVAVGDGASVVRTHGSSSSIGDGAAVGPFTYLRPGTALGADGKLGAFVEVKNSTIGTGTKVPHLTYVGDADIGEYSNIGASSVFVNYDGTSKRRTTVGSHVRTGSDTMFVAPVTIGDGAYTGAGTVVREDVPPGALAVSAGPQRNIENWVQRKRPGSPAAQASKRASEMACQQPTQPPDADQTP

Source Source

Source organism organism	Mycobacterium tuberculosis
NCBI taxonomy ID ncbi_taxonomy_id	1773
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	URIDINE-DIPHOSPHATE-N-ACETYLGLUCOSAMINE
Molecular weight formula_weight	607.4 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	147

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6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d3d8va1
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.68.1.0 — automated matches

Domain ID domain_id	d3d8va2
Class class	b — All beta proteins
Fold Fold fold	b.81 — Single-stranded left-handed beta-helix
Superfamily Superfamily superfamily	b.81.1 — Trimeric LpxA-like enzymes
Family Family family	b.81.1.0 — automated matches

CATH v4.4 (2 domains)

Domain ID domain_id	3d8vA01
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	3d8vA02
Class class	2 — Mainly Beta
Architecture architecture	160 — 3 Solenoid
Topology topology	10 — UDP N-Acetylglucosamine Acyltransferase; domain 1
Homologous superfamily homologous superfamily	10 — Hexapeptide repeat proteins

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Unit-cell length a length_a	114.238 Å
Unit-cell length b length_b	114.238 Å
Unit-cell length c length_c	361.796 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	18

Space group space_group	H 3 2
Space-group number int_tables_number	155
Crystal system crystal_system	—

Resolution resolution	2.550 Å
Low-resolution limit resolution_low	33.979 Å
R factor r_factor	0.2013
R_work r_work	0.1989
R_free r_free	0.2439

Crystal structure of GlmU from Mycobacterium tuberculosis in complex with uridine-diphosphate-N-acetylglucosamine

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

Bifunctional protein glmU

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

3d8v__assembly_1__model_1

3d8v__assembly_1__model_1 | I(q)

3d8v__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) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)

Crystal structure of GlmU from Mycobacterium tuberculosis in complex with uridine-diphosphate-N-acetylglucosamine

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

Bifunctional protein glmU

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

3d8v__assembly_1__model_1

3d8v__assembly_1__model_1 | I(q)

3d8v__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) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)