2dso

Crystal structure of D138N mutant 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	CALCIUM ION × 2 GLYCEROL × 1 water × 1	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	CALCIUM ION × 2 water × 1	Consistent with protein count
3	Protein monomer	Monomer	Protein 1	CALCIUM ION × 2 water × 1	Consistent with protein count
4	Protein monomer	Monomer	Protein 1	CALCIUM ION × 2 GLYCEROL × 2 water × 1	Consistent with protein count
5	Protein monomer	Monomer	Protein 1	CALCIUM ION × 2 water × 1	Consistent with protein count
6	Protein monomer	Monomer	Protein 1	CALCIUM ION × 2 water × 1	Consistent with protein count
7	Protein homooligomer	Homooligomer	Protein 3	CALCIUM ION × 6 GLYCEROL × 1 water × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q99QV3_STAAM
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

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	2dso
Deposition date deposition_date	2006-07-04
Structure title title	Crystal structure of D138N mutant 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.

2dso__assembly_3__model_1

Assembly 3 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

2dso__assembly_3__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2dso__assembly_3__model_1 | P(r) · Pending

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

Rg（Guinier）	19.37 Å
Rg (electron density)	18.22 Å
Total Rg	19.22 Å
Atom count	2528
Residues	323
Excluded volume	44951 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2dso__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`2dso__assembly_2__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`2dso__assembly_3__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`2dso__assembly_4__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
5	1	`2dso__assembly_5__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
6	1	`2dso__assembly_6__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
7	1	`2dso__assembly_7__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	Drp35
Molecular weight formula_weight	37136.7 kDa
EC 编号 ec_number	3.1.1.25
Mutation mutation	D138N
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	15988

MAMSQQDLPTLFYSGKSNSAVPIISESELQTITAEPWLEISKKGLQLEGLNFDRQGQLFLLDVFEGNIFKINPETKEIKRPFVSHKANPAAIKIHKDGRLFVCYLGDFKSTGGIFAATENGDNLQDIIEDLSTAYCINDMVFDSKGGFYFTDFRGYSTNPLGGVYYVSPDFRTVTPIIQNISVANGIALSTDEKVLWVTETTANRLHRIALEDDGVTIQPFGATIPYYFTGHEGPDSCCIDSDDNLYVAMYGQGRVLVFNKRGYPIGQILIPGRDEGHMLRSTHPQFIPGTNQLIICSNDIEMGGGSMLYTVNGFAKGHQSFQFQLEHHHHHH

Source Source

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

Entity 2 Entity 2 non-polymer

Description description	CALCIUM ION
Molecular weight formula_weight	40.1 kDa
Source method src_method	syn
Copy count entity_count	12

Entity 3 Entity 3 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	876

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6. Fold Classification (SCOP + CATH) 17 domains

SCOP 2.08 (11 domains)

Domain ID domain_id	d2dsoa1
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	d2dsoa2
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	d2dsob2
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	d2dsob3
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	d2dsoc2
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	d2dsoc3
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	d2dsod_
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	d2dsoe2
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	d2dsoe3
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	d2dsof2
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	d2dsof3
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

CATH v4.4 (6 domains)

Domain ID domain_id	2dsoA00
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	2dsoB00
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	2dsoC00
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	2dsoD00
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	2dsoE00
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	2dsoF00
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	76.548 Å
Unit-cell length b length_b	182.432 Å
Unit-cell length c length_c	81.454 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	115.58 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	12

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

Resolution resolution	2.100 Å
Low-resolution limit resolution_low	19.990 Å
R factor r_factor	0.1680
R_work r_work	0.1680
R_free r_free	0.2020

Crystal structure of D138N mutant 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

2dso__assembly_3__model_1

2dso__assembly_3__model_1 | I(q)

2dso__assembly_3__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) 17 domains

SCOP 2.08 (11 domains)

CATH v4.4 (6 domains)

7. Citations (1)

Crystal structure of D138N mutant 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

2dso__assembly_3__model_1

2dso__assembly_3__model_1 | I(q)

2dso__assembly_3__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) 17 domains

SCOP 2.08 (11 domains)

CATH v4.4 (6 domains)

7. Citations (1)