4wrk

The 3D structure of D95N mutant DUTPase from phage phi11 of S. aureus reveals the molecular details for the coordination of a structural Mg(II) ion

Method: X-RAY DIFFRACTION

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

DUTPase

Staphylococcus phage phi11

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 3	;2'-DEOXYURIDINE 5'-ALPHA,BETA-IMIDO-TRIPHOSPHATE ; × 3 MAGNESIUM ION × 3 water × 3	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 3	;2'-DEOXYURIDINE 5'-ALPHA,BETA-IMIDO-TRIPHOSPHATE ; × 3 MAGNESIUM ION × 3 water × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q8SDV3_BPPHA
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–169； UniProt 1–169 Author chain B； PDBConstruct 1–169； UniProt 1–169 Author chain C； PDBConstruct 1–169； UniProt 1–169 Author chain D； PDBConstruct 1–169； UniProt 1–169 Author chain E； PDBConstruct 1–169； UniProt 1–169 Author chain F； PDBConstruct 1–169； UniProt 1–169

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	4wrk
Deposition date deposition_date	2014-10-24
Structure title title	The 3D structure of D95N mutant DUTPase from phage phi11 of S. aureus reveals the molecular details for the coordination of a structural Mg(II) ion
Keywords keywords	Magnesium coordination mutant, hydrolase, jelly-roll; 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.

4wrk__assembly_1__model_1

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

Download this curve (.dat)

4wrk__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

4wrk__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	23.28 Å
Rg (electron density)	22.13 Å
Total Rg	22.92 Å
Atom count	3554
Residues	466
Excluded volume	62690 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`4wrk__assembly_1__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`4wrk__assembly_2__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 (4)

Entity 1 Entity 1 polymer

Description description	DUTPase
Molecular weight formula_weight	18386.6 kDa
Mutation mutation	D95N
Source method src_method	man
Copy count entity_count	6

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F
Atom count atom_count	7158

MTNTLQVRLLSENARMPERNHKTDAGYDIFSAETVVLEPQEKAVIKTDVAVSIPEGYVGLLTSRSGVSSKTHLVIETGKIDAGYHGNLGINIKNNAIASNGYITPGVFDIKGEIDLSDAIRQYGTYQINEGDKLAQLVIVPIWTPELKQVEEFESVSERGEKGFGSSGV

Source Source

Source organism organism	Staphylococcus phage phi11
NCBI taxonomy ID ncbi_taxonomy_id	12360
Host organism host_organism	Escherichia coli

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	6

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	6

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	101

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6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

Domain ID domain_id	d4wrka_
Class class	b — All beta proteins
Fold Fold fold	b.85 — beta-clip
Superfamily Superfamily superfamily	b.85.4 — dUTPase-like
Family Family family	b.85.4.0 — automated matches

Domain ID domain_id	d4wrkb_
Class class	b — All beta proteins
Fold Fold fold	b.85 — beta-clip
Superfamily Superfamily superfamily	b.85.4 — dUTPase-like
Family Family family	b.85.4.0 — automated matches

Domain ID domain_id	d4wrkc_
Class class	b — All beta proteins
Fold Fold fold	b.85 — beta-clip
Superfamily Superfamily superfamily	b.85.4 — dUTPase-like
Family Family family	b.85.4.0 — automated matches

Domain ID domain_id	d4wrkd_
Class class	b — All beta proteins
Fold Fold fold	b.85 — beta-clip
Superfamily Superfamily superfamily	b.85.4 — dUTPase-like
Family Family family	b.85.4.0 — automated matches

Domain ID domain_id	d4wrke_
Class class	b — All beta proteins
Fold Fold fold	b.85 — beta-clip
Superfamily Superfamily superfamily	b.85.4 — dUTPase-like
Family Family family	b.85.4.0 — automated matches

Domain ID domain_id	d4wrkf_
Class class	b — All beta proteins
Fold Fold fold	b.85 — beta-clip
Superfamily Superfamily superfamily	b.85.4 — dUTPase-like
Family Family family	b.85.4.0 — automated matches

CATH v4.4 (6 domains)

Domain ID domain_id	4wrkA00
Class class	2 — Mainly Beta
Architecture architecture	70 — Distorted Sandwich
Topology topology	40 — Deoxyuridine 5'-Triphosphate Nucleotidohydrolase; Chain A
Homologous superfamily homologous superfamily	10 — Deoxyuridine triphosphatase (dUTPase)

Domain ID domain_id	4wrkB00
Class class	2 — Mainly Beta
Architecture architecture	70 — Distorted Sandwich
Topology topology	40 — Deoxyuridine 5'-Triphosphate Nucleotidohydrolase; Chain A
Homologous superfamily homologous superfamily	10 — Deoxyuridine triphosphatase (dUTPase)

Domain ID domain_id	4wrkC00
Class class	2 — Mainly Beta
Architecture architecture	70 — Distorted Sandwich
Topology topology	40 — Deoxyuridine 5'-Triphosphate Nucleotidohydrolase; Chain A
Homologous superfamily homologous superfamily	10 — Deoxyuridine triphosphatase (dUTPase)

Domain ID domain_id	4wrkD00
Class class	2 — Mainly Beta
Architecture architecture	70 — Distorted Sandwich
Topology topology	40 — Deoxyuridine 5'-Triphosphate Nucleotidohydrolase; Chain A
Homologous superfamily homologous superfamily	10 — Deoxyuridine triphosphatase (dUTPase)

Domain ID domain_id	4wrkE00
Class class	2 — Mainly Beta
Architecture architecture	70 — Distorted Sandwich
Topology topology	40 — Deoxyuridine 5'-Triphosphate Nucleotidohydrolase; Chain A
Homologous superfamily homologous superfamily	10 — Deoxyuridine triphosphatase (dUTPase)

Domain ID domain_id	4wrkF00
Class class	2 — Mainly Beta
Architecture architecture	70 — Distorted Sandwich
Topology topology	40 — Deoxyuridine 5'-Triphosphate Nucleotidohydrolase; Chain A
Homologous superfamily homologous superfamily	10 — Deoxyuridine triphosphatase (dUTPase)

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Unit-cell length a length_a	108.420 Å
Unit-cell length b length_b	108.420 Å
Unit-cell length c length_c	167.050 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	48

Space group space_group	P 43 21 2
Space-group number int_tables_number	96
Crystal system crystal_system	—

Resolution resolution	2.900 Å
Low-resolution limit resolution_low	19.570 Å
R factor r_factor	0.2110
R_work r_work	0.2085
R_free r_free	0.2583

The 3D structure of D95N mutant DUTPase from phage phi11 of S. aureus reveals the molecular details for the coordination of a structural Mg(II) ion

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

DUTPase

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

4wrk__assembly_1__model_1

4wrk__assembly_1__model_1 | I(q)

4wrk__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) 12 domains

SCOP 2.08 (6 domains)

CATH v4.4 (6 domains)

7. Citations (1)

The 3D structure of D95N mutant DUTPase from phage phi11 of S. aureus reveals the molecular details for the coordination of a structural Mg(II) ion

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

DUTPase

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

4wrk__assembly_1__model_1

4wrk__assembly_1__model_1 | I(q)

4wrk__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) 12 domains

SCOP 2.08 (6 domains)

CATH v4.4 (6 domains)

7. Citations (1)