SAXSdb — 2pq7

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

Predicted HD superfamily hydrolase

uncultured Thermotogales bacterium

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	FE (III) ION × 4 CHLORIDE ION × 2 PHOSPHATE ION × 4 (4S)-2-METHYL-2,4-PENTANEDIOL × 2 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q1EM40_9BACT
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–220； UniProt 1–219

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	2pq7
Deposition date deposition_date	2007-05-01
Structure title title	Crystal structure of predicted HD superfamily hydrolase (104161995) from uncultured Thermotogales bacterium at 1.45 A resolution
Keywords keywords	;104161995, HD domain, predicted HD superfamily hydrolase, Structural Genomics, Joint Center for Structural Genomics, JCSG, Protein Structure Initiative, PSI-2, 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.

2pq7__assembly_1__model_1

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

Download this curve (.dat)

2pq7__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2pq7__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	27.36 Å
Rg (electron density)	27.43 Å
Total Rg	28.14 Å
Atom count	2728
Residues	338
Excluded volume	48650 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2pq7__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 (6)

Entity 1 Entity 1 polymer

Description description	Predicted HD superfamily hydrolase
Molecular weight formula_weight	24962.5 kDa
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	1613

GMNLTELMERIPHLREILNIVREAFKDYDDPAHDISHTFRVMENASEIASREKCDLQKAIIAALLHDIKRPHEALTGVDHAESGAEYASGLLPTMGFDISFVAEVSKAIRSHRYSGGLTPTSLTGKILQDADRLDAIGAVAIARVFSYSGKTGTPLHSLQFSPRSSYSGNSRSSINHFHEKILKIRPETFWTETARKMAEDRYSFVVEFVQRFLAEWGQI

Source Source

Source organism organism	uncultured Thermotogales bacterium
NCBI taxonomy ID ncbi_taxonomy_id	221214
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	FE (III) ION
Molecular weight formula_weight	55.8 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	1

Entity 4 Entity 4 non-polymer

Description description	PHOSPHATE ION
Molecular weight formula_weight	95.0 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 non-polymer

Description description	(4S)-2-METHYL-2,4-PENTANEDIOL
Molecular weight formula_weight	118.2 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	148

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6. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d2pq7a1
Class class	a — All alpha proteins
Fold Fold fold	a.211 — HD-domain/PDEase-like
Superfamily Superfamily superfamily	a.211.1 — HD-domain/PDEase-like
Family Family family	a.211.1.1 — HD domain

CATH v4.4 (1 domains)

Domain ID domain_id	2pq7A00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	3210 — Hypothetical protein af1432
Homologous superfamily homologous superfamily	10 — Hypothetical protein af1432

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Unit-cell length a length_a	138.518 Å
Unit-cell length b length_b	40.662 Å
Unit-cell length c length_c	37.789 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	95.32 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	1.450 Å
Low-resolution limit resolution_low	27.441 Å
R factor r_factor	0.1830
R_work r_work	0.1830
R_free r_free	0.1930

Crystal structure of predicted HD superfamily hydrolase (104161995) from uncultured Thermotogales bacterium at 1.45 A resolution

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

Predicted HD superfamily hydrolase

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

2pq7__assembly_1__model_1

2pq7__assembly_1__model_1 | I(q)

2pq7__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 (6)

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 water

6. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

CATH v4.4 (1 domains)

7. Citations (1)

Crystal structure of predicted HD superfamily hydrolase (104161995) from uncultured Thermotogales bacterium at 1.45 A resolution

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

Predicted HD superfamily hydrolase

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

2pq7__assembly_1__model_1

2pq7__assembly_1__model_1 | I(q)

2pq7__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 (6)

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 water

6. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

CATH v4.4 (1 domains)

7. Citations (1)