2dg0

Crystal structure of Drp35, a 35kDa drug responsive protein from Staphylococcus aureus

Method: X-RAY DIFFRACTION

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

DrP35

Staphylococcus aureus

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	water × 1	Consistent with protein count
10	Protein monomer	Monomer	Protein 1	water × 1	Consistent with protein count
11	Protein monomer	Monomer	Protein 1	water × 1	Consistent with protein count
12	Protein monomer	Monomer	Protein 1	water × 1	Consistent with protein count
13	Protein homooligomer	Homooligomer	Protein 3	water × 3	Consistent with protein count
14	Protein homooligomer	Homooligomer	Protein 3	water × 3	Consistent with protein count
15	Protein homooligomer	Homooligomer	Protein 3	water × 3	Consistent with protein count
16	Protein homooligomer	Homooligomer	Protein 3	water × 3	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	water × 1	Consistent with protein count
3	Protein monomer	Monomer	Protein 1	water × 1	Consistent with protein count
4	Protein monomer	Monomer	Protein 1	water × 1	Consistent with protein count
5	Protein monomer	Monomer	Protein 1	water × 1	Consistent with protein count
6	Protein monomer	Monomer	Protein 1	water × 1	Consistent with protein count
7	Protein monomer	Monomer	Protein 1	water × 1	Consistent with protein count
8	Protein monomer	Monomer	Protein 1	water × 1	Consistent with protein count
9	Protein monomer	Monomer	Protein 1	water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	DRP35_STAAU
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 3–325； UniProt 2–324 Author chain B； PDBConstruct 3–325； UniProt 2–324 Author chain C； PDBConstruct 3–325； UniProt 2–324 Author chain D； PDBConstruct 3–325； UniProt 2–324 Author chain E； PDBConstruct 3–325； UniProt 2–324 Author chain F； PDBConstruct 3–325； UniProt 2–324 Author chain G； PDBConstruct 3–325； UniProt 2–324 Author chain H； PDBConstruct 3–325； UniProt 2–324 Author chain I； PDBConstruct 3–325； UniProt 2–324 Author chain J； PDBConstruct 3–325； UniProt 2–324 Author chain K； PDBConstruct 3–325； UniProt 2–324 Author chain L； PDBConstruct 3–325； UniProt 2–324

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	2dg0
Deposition date deposition_date	2006-03-07
Structure title title	Crystal structure of Drp35, a 35kDa drug responsive protein from Staphylococcus aureus
Keywords keywords	BETA PROPELLER, 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.

2dg0__assembly_6__model_1

Assembly 6 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

2dg0__assembly_6__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2dg0__assembly_6__model_1 | P(r) · Pending

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

Rg（Guinier）	19.31 Å
Rg (electron density)	18.18 Å
Total Rg	19.16 Å
Atom count	2512
Residues	316
Excluded volume	44651 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2dg0__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`2dg0__assembly_2__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`2dg0__assembly_3__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`2dg0__assembly_4__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
5	1	`2dg0__assembly_5__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
6	1	`2dg0__assembly_6__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
7	1	`2dg0__assembly_7__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
8	1	`2dg0__assembly_8__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
9	1	`2dg0__assembly_9__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
10	1	`2dg0__assembly_10__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
11	1	`2dg0__assembly_11__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
12	1	`2dg0__assembly_12__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
13	1	`2dg0__assembly_13__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
14	1	`2dg0__assembly_14__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
15	1	`2dg0__assembly_15__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
16	1	`2dg0__assembly_16__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 (2)

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6. Fold Classification (SCOP + CATH) 27 domains

SCOP 2.08 (15 domains)

Domain ID domain_id	d2dg0a1
Class class	b — All beta proteins
Fold Fold fold	b.68 — 6-bladed beta-propeller
Superfamily Superfamily superfamily	b.68.6 — Calcium-dependent phosphotriesterase
Family Family family	b.68.6.1 — SGL-like

Domain ID domain_id	d2dg0a2
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	d2dg0b_
Class class	b — All beta proteins
Fold Fold fold	b.68 — 6-bladed beta-propeller
Superfamily Superfamily superfamily	b.68.6 — Calcium-dependent phosphotriesterase
Family Family family	b.68.6.1 — SGL-like

Domain ID domain_id	d2dg0c_
Class class	b — All beta proteins
Fold Fold fold	b.68 — 6-bladed beta-propeller
Superfamily Superfamily superfamily	b.68.6 — Calcium-dependent phosphotriesterase
Family Family family	b.68.6.1 — SGL-like

Domain ID domain_id	d2dg0d_
Class class	b — All beta proteins
Fold Fold fold	b.68 — 6-bladed beta-propeller
Superfamily Superfamily superfamily	b.68.6 — Calcium-dependent phosphotriesterase
Family Family family	b.68.6.1 — SGL-like

Domain ID domain_id	d2dg0e2
Class class	b — All beta proteins
Fold Fold fold	b.68 — 6-bladed beta-propeller
Superfamily Superfamily superfamily	b.68.6 — Calcium-dependent phosphotriesterase
Family Family family	b.68.6.1 — SGL-like

Domain ID domain_id	d2dg0e3
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	d2dg0f_
Class class	b — All beta proteins
Fold Fold fold	b.68 — 6-bladed beta-propeller
Superfamily Superfamily superfamily	b.68.6 — Calcium-dependent phosphotriesterase
Family Family family	b.68.6.1 — SGL-like

Domain ID domain_id	d2dg0g_
Class class	b — All beta proteins
Fold Fold fold	b.68 — 6-bladed beta-propeller
Superfamily Superfamily superfamily	b.68.6 — Calcium-dependent phosphotriesterase
Family Family family	b.68.6.1 — SGL-like

Domain ID domain_id	d2dg0h_
Class class	b — All beta proteins
Fold Fold fold	b.68 — 6-bladed beta-propeller
Superfamily Superfamily superfamily	b.68.6 — Calcium-dependent phosphotriesterase
Family Family family	b.68.6.1 — SGL-like

Domain ID domain_id	d2dg0i_
Class class	b — All beta proteins
Fold Fold fold	b.68 — 6-bladed beta-propeller
Superfamily Superfamily superfamily	b.68.6 — Calcium-dependent phosphotriesterase
Family Family family	b.68.6.1 — SGL-like

Domain ID domain_id	d2dg0j2
Class class	b — All beta proteins
Fold Fold fold	b.68 — 6-bladed beta-propeller
Superfamily Superfamily superfamily	b.68.6 — Calcium-dependent phosphotriesterase
Family Family family	b.68.6.1 — SGL-like

Domain ID domain_id	d2dg0j3
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	d2dg0k_
Class class	b — All beta proteins
Fold Fold fold	b.68 — 6-bladed beta-propeller
Superfamily Superfamily superfamily	b.68.6 — Calcium-dependent phosphotriesterase
Family Family family	b.68.6.1 — SGL-like

Domain ID domain_id	d2dg0l_
Class class	b — All beta proteins
Fold Fold fold	b.68 — 6-bladed beta-propeller
Superfamily Superfamily superfamily	b.68.6 — Calcium-dependent phosphotriesterase
Family Family family	b.68.6.1 — SGL-like

CATH v4.4 (12 domains)

Domain ID domain_id	2dg0A00
Class class	2 — Mainly Beta
Architecture architecture	120 — 6 Propeller
Topology topology	10 — Neuraminidase
Homologous superfamily homologous superfamily	30 — TolB, C-terminal domain

Domain ID domain_id	2dg0B00
Class class	2 — Mainly Beta
Architecture architecture	120 — 6 Propeller
Topology topology	10 — Neuraminidase
Homologous superfamily homologous superfamily	30 — TolB, C-terminal domain

Domain ID domain_id	2dg0C00
Class class	2 — Mainly Beta
Architecture architecture	120 — 6 Propeller
Topology topology	10 — Neuraminidase
Homologous superfamily homologous superfamily	30 — TolB, C-terminal domain

Domain ID domain_id	2dg0D00
Class class	2 — Mainly Beta
Architecture architecture	120 — 6 Propeller
Topology topology	10 — Neuraminidase
Homologous superfamily homologous superfamily	30 — TolB, C-terminal domain

Domain ID domain_id	2dg0E00
Class class	2 — Mainly Beta
Architecture architecture	120 — 6 Propeller
Topology topology	10 — Neuraminidase
Homologous superfamily homologous superfamily	30 — TolB, C-terminal domain

Domain ID domain_id	2dg0F00
Class class	2 — Mainly Beta
Architecture architecture	120 — 6 Propeller
Topology topology	10 — Neuraminidase
Homologous superfamily homologous superfamily	30 — TolB, C-terminal domain

Domain ID domain_id	2dg0G00
Class class	2 — Mainly Beta
Architecture architecture	120 — 6 Propeller
Topology topology	10 — Neuraminidase
Homologous superfamily homologous superfamily	30 — TolB, C-terminal domain

Domain ID domain_id	2dg0H00
Class class	2 — Mainly Beta
Architecture architecture	120 — 6 Propeller
Topology topology	10 — Neuraminidase
Homologous superfamily homologous superfamily	30 — TolB, C-terminal domain

Domain ID domain_id	2dg0I00
Class class	2 — Mainly Beta
Architecture architecture	120 — 6 Propeller
Topology topology	10 — Neuraminidase
Homologous superfamily homologous superfamily	30 — TolB, C-terminal domain

Domain ID domain_id	2dg0J00
Class class	2 — Mainly Beta
Architecture architecture	120 — 6 Propeller
Topology topology	10 — Neuraminidase
Homologous superfamily homologous superfamily	30 — TolB, C-terminal domain

Domain ID domain_id	2dg0K00
Class class	2 — Mainly Beta
Architecture architecture	120 — 6 Propeller
Topology topology	10 — Neuraminidase
Homologous superfamily homologous superfamily	30 — TolB, C-terminal domain

Domain ID domain_id	2dg0L00
Class class	2 — Mainly Beta
Architecture architecture	120 — 6 Propeller
Topology topology	10 — Neuraminidase
Homologous superfamily homologous superfamily	30 — TolB, C-terminal domain

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Unit-cell length a length_a	86.089 Å
Unit-cell length b length_b	146.062 Å
Unit-cell length c length_c	151.947 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	93.39 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	24

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

Resolution resolution	2.400 Å
Low-resolution limit resolution_low	15.000 Å
R factor r_factor	0.2000
R_work r_work	0.2000
R_free r_free	0.2220

Description description	DrP35
Molecular weight formula_weight	37466.0 kDa
EC 编号 ec_number	3.1.1.25
Source method src_method	man
Copy count entity_count	12

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F,G,H,I,J,K,L
Atom count atom_count	31391

Crystal structure of Drp35, a 35kDa drug responsive protein from Staphylococcus aureus

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

DrP35

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

2dg0__assembly_6__model_1

2dg0__assembly_6__model_1 | I(q)

2dg0__assembly_6__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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 water

6. Fold Classification (SCOP + CATH) 27 domains

SCOP 2.08 (15 domains)

CATH v4.4 (12 domains)

7. Citations (1)

Source organism organism	Staphylococcus aureus
NCBI taxonomy ID ncbi_taxonomy_id	1280
Host organism host_organism	Escherichia coli

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	1295

Crystal structure of Drp35, a 35kDa drug responsive protein from Staphylococcus aureus

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

DrP35

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

2dg0__assembly_6__model_1

2dg0__assembly_6__model_1 | I(q)

2dg0__assembly_6__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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 water

6. Fold Classification (SCOP + CATH) 27 domains

SCOP 2.08 (15 domains)

CATH v4.4 (12 domains)

7. Citations (1)