SAXSdb — 5hyl

▼

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

DR2231

Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422)

UniProt Q9RS96

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	;2'-DEOXYURIDINE 5'-ALPHA,BETA-IMIDO-TRIPHOSPHATE ; × 1 MAGNESIUM ION × 1 water × 2	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 2	;2'-DEOXYURIDINE 5'-ALPHA,BETA-IMIDO-TRIPHOSPHATE ; × 1 MAGNESIUM ION × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q9RS96_DEIRA
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 6–151； UniProt 1–146 Author chain B； PDBConstruct 6–151； UniProt 1–146 Author chain C； PDBConstruct 6–151； UniProt 1–146 Author chain D； PDBConstruct 6–151； UniProt 1–146

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	5hyl
Deposition date deposition_date	2016-02-01
Structure title title	Crystal structure of DR2231_E47A mutant in complex with dUMPNPP and magnesium
Keywords keywords	alpha helix, hydrolase; HYDROLASE
Experimental Method method	X-RAY DIFFRACTION

▼

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.

5hyl__assembly_2__model_1

Assembly 2 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

5hyl__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

5hyl__assembly_2__model_1 | P(r) · Pending

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

Rg（Guinier）	20.18 Å
Rg (electron density)	18.96 Å
Total Rg	19.91 Å
Atom count	2188
Residues	283
Excluded volume	38385 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`5hyl__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`5hyl__assembly_2__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download

▶

4. Crystallography and Experiment 4. Crystallography & Experiment

▶

5. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	DR2231
Molecular weight formula_weight	16363.4 kDa
Mutation mutation	E47A
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	5305

IDPFTMSDLPCPPTNAERLHEFHRAIGAATPERPTPPPPELLRLRQTLLDEASAEVRAEIDHLLARQAAGEALSAGDLAPLAHELADLLYVTYGALDQLGIDADAVFAEVHRANLSKASGPRRADGKQLKPEGWRPADVRGVIERLQHAPA

Source Source

Source organism organism	Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422)
NCBI taxonomy ID ncbi_taxonomy_id	243230
Host organism host_organism	Escherichia coli BL21

Entity 2 Entity 2 non-polymer

Description description	;2'-DEOXYURIDINE 5'-ALPHA,BETA-IMIDO-TRIPHOSPHATE ;
Molecular weight formula_weight	467.2 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	913

▼

6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id	5hylA00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	3420 — putative ntp pyrophosphohydrolase like fold
Homologous superfamily homologous superfamily	10 — putative ntp pyrophosphohydrolase like domain

Domain ID domain_id	5hylB00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	3420 — putative ntp pyrophosphohydrolase like fold
Homologous superfamily homologous superfamily	10 — putative ntp pyrophosphohydrolase like domain

Domain ID domain_id	5hylC00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	3420 — putative ntp pyrophosphohydrolase like fold
Homologous superfamily homologous superfamily	10 — putative ntp pyrophosphohydrolase like domain

Domain ID domain_id	5hylD00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	3420 — putative ntp pyrophosphohydrolase like fold
Homologous superfamily homologous superfamily	10 — putative ntp pyrophosphohydrolase like domain

▶

Unit-cell length a length_a	149.063 Å
Unit-cell length b length_b	77.822 Å
Unit-cell length c length_c	52.713 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	16

Space group space_group	P 21 21 2
Space-group number int_tables_number	18
Crystal system crystal_system	—

Resolution resolution	1.800 Å
Low-resolution limit resolution_low	43.037 Å
R factor r_factor	0.1625
R_work r_work	0.1603
R_free r_free	0.2051

Crystal structure of DR2231_E47A mutant in complex with dUMPNPP and magnesium

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

DR2231

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

5hyl__assembly_2__model_1

5hyl__assembly_2__model_1 | I(q)

5hyl__assembly_2__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) 4 domains

CATH v4.4 (4 domains)

7. Citations (1)

Crystal structure of DR2231_E47A mutant in complex with dUMPNPP and magnesium

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

DR2231

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

5hyl__assembly_2__model_1

5hyl__assembly_2__model_1 | I(q)

5hyl__assembly_2__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) 4 domains

CATH v4.4 (4 domains)

7. Citations (1)