SAXSdb — 2i5e

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

Hypothetical protein MM_2497

Methanosarcina mazei

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 5 DI(HYDROXYETHYL)ETHER × 3 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q8PU52_METMA
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 4–211； UniProt 1–208 Author chain B； PDBConstruct 4–211； UniProt 1–208

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	2i5e
Deposition date deposition_date	2006-08-24
Structure title title	Crystal Structure of a Protein of Unknown Function MM2497 from Methanosarcina mazei Go1, Probable Nucleotidyltransferase
Keywords keywords	;APC86122, Methanosarcina mazei Go1, Hypothetic Protein, Structural Genomics, PSI-2, Protein Structure Initiative, Midwest Center for Structural Genomics, MCSG, UNKNOWN FUNCTION ;; STRUCTURAL GENOMICS, UNKNOWN FUNCTION
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.

2i5e__assembly_1__model_1

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

Download this curve (.dat)

2i5e__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2i5e__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	23.41 Å
Rg (electron density)	22.42 Å
Total Rg	23.21 Å
Atom count	3323
Residues	410
Excluded volume	60055 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2i5e__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 (4)

Entity 1 Entity 1 polymer

Description description	Hypothetical protein MM_2497
Molecular weight formula_weight	23585.2 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	3496

SNAMRAVIPYKKAGAKSRLSPVLSLQEREEFVELMLNQVISSLKGAGIEQVDILSPSVYGLEEMTEARVLLDEKDLNEALNRYLKEAEEPVLIVMADLPLLSPEHIKEISSTEKDVCIVPGKGGGTNALFIKNPSKYRVKYYGSSFLTHCSIATDSGQDFEIYDSFMAGTDIDEPEDLVELLIHGKGAAKDYIESKFRLEVKKGRVGLVPL

Source Source

Source organism organism	Methanosarcina mazei
NCBI taxonomy ID ncbi_taxonomy_id	192952
Host organism host_organism	Escherichia coli BL21

Entity 2 Entity 2 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	5

Entity 3 Entity 3 non-polymer

Description description	DI(HYDROXYETHYL)ETHER
Molecular weight formula_weight	106.1 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	173

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6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d2i5ea1
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.68.1.21 — MM2497-like

Domain ID domain_id	d2i5ea2
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	d2i5eb2
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.68.1.21 — MM2497-like

Domain ID domain_id	d2i5eb3
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	2i5eA01
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	2i5eA02
Class class	6 — Special
Architecture architecture	10 — Helix non-globular
Topology topology	140 — Helix Hairpins
Homologous superfamily homologous superfamily	50 —

Domain ID domain_id	2i5eB01
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	2i5eB02
Class class	6 — Special
Architecture architecture	10 — Helix non-globular
Topology topology	140 — Helix Hairpins
Homologous superfamily homologous superfamily	50 —

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Unit-cell length a length_a	43.797 Å
Unit-cell length b length_b	100.482 Å
Unit-cell length c length_c	54.877 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	106.15 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	2.100 Å
Low-resolution limit resolution_low	38.810 Å
R factor r_factor	0.1946
R_work r_work	0.1916
R_free r_free	0.2487

Crystal Structure of a Protein of Unknown Function MM2497 from Methanosarcina mazei Go1, Probable Nucleotidyltransferase

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

Hypothetical protein MM_2497

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

2i5e__assembly_1__model_1

2i5e__assembly_1__model_1 | I(q)

2i5e__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 (4)

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 water

6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

7. Citations (1)

Crystal Structure of a Protein of Unknown Function MM2497 from Methanosarcina mazei Go1, Probable Nucleotidyltransferase

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

Hypothetical protein MM_2497

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

2i5e__assembly_1__model_1

2i5e__assembly_1__model_1 | I(q)

2i5e__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 (4)

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 water

6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

7. Citations (1)