SAXSdb — 2ntk

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

IMP cyclohydrolase

Methanothermobacter thermautotrophicus

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 4	INOSINIC ACID × 4 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	PURO_METTH
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 21–222； UniProt 1–202 Author chain B； PDBConstruct 21–222； UniProt 1–202 Author chain C； PDBConstruct 21–222； UniProt 1–202 Author chain D； PDBConstruct 21–222； UniProt 1–202

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	2ntk
Deposition date deposition_date	2006-11-07
Structure title title	Crystal structure of PurO/IMP from Methanothermobacter thermoautotrophicus
Keywords keywords	alpha-beta-beta-alpha NTN hydrolase fold, HYDROLASE; HYDROLASE
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.

2ntk__assembly_1__model_1

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

Download this curve (.dat)

2ntk__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2ntk__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	28.56 Å
Rg (electron density)	27.34 Å
Total Rg	28.06 Å
Atom count	6271
Residues	812
Excluded volume	110160 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2ntk__assembly_1__model_1`	tetrameric （4）	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	IMP cyclohydrolase
Molecular weight formula_weight	24030.8 kDa
EC 编号 ec_number	3.5.4.10
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	6471

MGSSHHHHHHSSGLVPRGSHMYLGRILAVGRNSNGSFVAYRVSSRSFPNRTTSIQEERVAVVPVEGHERDVFRNPYIAYNCIRIVGDTAVVSNGSHTDTIADKVALGMNLRDAIGLSLLAMDYEKDELNTPRIAAAINGSEAFIGIVTADGLMVSRVPEETPVYISTYEQTEPAATEFKAGSPEEAAEFILKGGEFAAFTHPVTAAAAFNDGEGWNLATREM

Source Source

Source organism organism	Methanothermobacter thermautotrophicus
NCBI taxonomy ID ncbi_taxonomy_id	145262
Host organism host_organism	Escherichia coli BL21

Entity 2 Entity 2 non-polymer

Description description	INOSINIC ACID
Molecular weight formula_weight	348.2 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	200

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6. Fold Classification (SCOP + CATH) 9 domains

SCOP 2.08 (5 domains)

Domain ID domain_id	d2ntka2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.153 — Ntn hydrolase-like
Superfamily Superfamily superfamily	d.153.2 — Archaeal IMP cyclohydrolase PurO
Family Family family	d.153.2.1 — Archaeal IMP cyclohydrolase PurO

Domain ID domain_id	d2ntka3
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	d2ntkb_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.153 — Ntn hydrolase-like
Superfamily Superfamily superfamily	d.153.2 — Archaeal IMP cyclohydrolase PurO
Family Family family	d.153.2.1 — Archaeal IMP cyclohydrolase PurO

Domain ID domain_id	d2ntkc_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.153 — Ntn hydrolase-like
Superfamily Superfamily superfamily	d.153.2 — Archaeal IMP cyclohydrolase PurO
Family Family family	d.153.2.1 — Archaeal IMP cyclohydrolase PurO

Domain ID domain_id	d2ntkd_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.153 — Ntn hydrolase-like
Superfamily Superfamily superfamily	d.153.2 — Archaeal IMP cyclohydrolase PurO
Family Family family	d.153.2.1 — Archaeal IMP cyclohydrolase PurO

CATH v4.4 (4 domains)

Domain ID domain_id	2ntkA00
Class class	3 — Alpha Beta
Architecture architecture	60 — 4-Layer Sandwich
Topology topology	20 — Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1
Homologous superfamily homologous superfamily	20 — Inosine monophosphate cyclohydrolase-like

Domain ID domain_id	2ntkB00
Class class	3 — Alpha Beta
Architecture architecture	60 — 4-Layer Sandwich
Topology topology	20 — Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1
Homologous superfamily homologous superfamily	20 — Inosine monophosphate cyclohydrolase-like

Domain ID domain_id	2ntkC00
Class class	3 — Alpha Beta
Architecture architecture	60 — 4-Layer Sandwich
Topology topology	20 — Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1
Homologous superfamily homologous superfamily	20 — Inosine monophosphate cyclohydrolase-like

Domain ID domain_id	2ntkD00
Class class	3 — Alpha Beta
Architecture architecture	60 — 4-Layer Sandwich
Topology topology	20 — Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1
Homologous superfamily homologous superfamily	20 — Inosine monophosphate cyclohydrolase-like

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Unit-cell length a length_a	85.975 Å
Unit-cell length b length_b	85.975 Å
Unit-cell length c length_c	124.442 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
Space-group number int_tables_number	145
Crystal system crystal_system	—

Resolution resolution	2.030 Å
Low-resolution limit resolution_low	27.450 Å
R factor r_factor	0.2180
R_work r_work	0.2180
R_free r_free	0.2450

Crystal structure of PurO/IMP from Methanothermobacter thermoautotrophicus

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

IMP cyclohydrolase

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

2ntk__assembly_1__model_1

2ntk__assembly_1__model_1 | I(q)

2ntk__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) 9 domains

SCOP 2.08 (5 domains)

CATH v4.4 (4 domains)

7. Citations (1)

Crystal structure of PurO/IMP from Methanothermobacter thermoautotrophicus

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

IMP cyclohydrolase

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

2ntk__assembly_1__model_1

2ntk__assembly_1__model_1 | I(q)

2ntk__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) 9 domains

SCOP 2.08 (5 domains)

CATH v4.4 (4 domains)

7. Citations (1)