SAXSdb — 6x1g

▼

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

ULP_PROTEASE domain-containing protein

Orientia tsutsugamushi

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	Ras-related C3 botulinum toxin substrate 1 × 1 （P63000） water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	Ras-related C3 botulinum toxin substrate 1 × 1 （P63000） 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	B3CVM3_ORITI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–213； UniProt 548–759 Author chain C； PDBConstruct 2–213； UniProt 548–759

Ras-related C3 botulinum toxin substrate 1

Homo sapiens

UniProt P63000

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	ULP_PROTEASE domain-containing protein × 1 （B3CVM3） water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	ULP_PROTEASE domain-containing protein × 1 （B3CVM3） 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	RAC1_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–177； UniProt 1–177 Author chain D； PDBConstruct 1–177； UniProt 1–177

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	6x1g
Deposition date deposition_date	2020-05-18
Structure title title	Crystal structure of a GEF domain from the Orientia tsutsugamushi protein OtDUB in complex with Rac1
Keywords keywords	;guanine nucleotide exchange factor, GEF, Rac1, GTPase, Orientia tsutsugamushi, scrub typhus, SIGNALING PROTEIN, SIGNALING PROTEIN-HYDROLASE complex ;; SIGNALING PROTEIN/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.

6x1g__assembly_1__model_1

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

Download this curve (.dat)

6x1g__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

6x1g__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	23.20 Å
Rg (electron density)	22.12 Å
Total Rg	23.05 Å
Atom count	3133
Residues	394
Excluded volume	56065 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`6x1g__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`6x1g__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	ULP_PROTEASE domain-containing protein
Molecular weight formula_weight	25190.5 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,C
Atom count atom_count	6578

MERLVKKVTSNLETELKFFKGRLVQELMQIVKNENGRIDHTSKNWQESASVLLNSQEKGAVSLAEVERAVSKMTQKLRDQKVSEEEVVNIESKLKFERASLEAKLFDDNEIKELINKRIKEDALRAIPFLGSDSESFMEKISPFVKLPDDSYSLLKANDKHHPFQNILYSNALKFFADSSDIGYLNDDSLKNLTPENLNAFEQAVAADIDKLMHHHHHH

Source Source

Source organism organism	Orientia tsutsugamushi
Common name common_name	Rickettsia tsutsugamushi
NCBI taxonomy ID ncbi_taxonomy_id	334380
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Ras-related C3 botulinum toxin substrate 1
Molecular weight formula_weight	20539.6 kDa
EC 编号 ec_number	3.6.5.2
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,D

MQAIKCVVVGDGAVGKTCLLISYTTNAFPGEYIPTVFDNYSANVMVDGKPVNLGLWDTAGQEDYDRLRPLSYPQTDVFLICFSLVSPASFENVRAKWYPEVRHHCPNTPIILVGTKLDLRDDKDTIEKLKEKKLTPITYPQGLAMAKEIGAVKYLECSALTQRGLKTVFDEAIRAVLHHHHHH

Source Source

Source organism organism	Homo sapiens
Common name common_name	Human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Escherichia coli

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	1

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	311

▼

6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d6x1gb1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.37 — P-loop containing nucleoside triphosphate hydrolases
Superfamily Superfamily superfamily	c.37.1 — P-loop containing nucleoside triphosphate hydrolases
Family Family family	c.37.1.8 — G proteins

Domain ID domain_id	d6x1gb2
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	d6x1gd1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.37 — P-loop containing nucleoside triphosphate hydrolases
Superfamily Superfamily superfamily	c.37.1 — P-loop containing nucleoside triphosphate hydrolases
Family Family family	c.37.1.8 — G proteins

Domain ID domain_id	d6x1gd2
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

▶

Unit-cell length a length_a	50.063 Å
Unit-cell length b length_b	54.160 Å
Unit-cell length c length_c	94.004 Å
Unit-cell angle α angle_alpha	83.37 °
Unit-cell angle β angle_beta	76.34 °
Unit-cell angle γ angle_gamma	62.52 °
Molecules per unit cell Z z_pdb	2

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

Resolution resolution	1.600 Å
Low-resolution limit resolution_low	48.050 Å
R factor r_factor	0.1828
R_work r_work	0.1810
R_free r_free	0.2182

Crystal structure of a GEF domain from the Orientia tsutsugamushi protein OtDUB in complex with Rac1

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

ULP_PROTEASE domain-containing protein

State in the Current Structure

Other States of the Same Protein in the Database

Ras-related C3 botulinum toxin substrate 1

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

6x1g__assembly_1__model_1

6x1g__assembly_1__model_1 | I(q)

6x1g__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 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (4 domains)

7. Citations (1)

Crystal structure of a GEF domain from the Orientia tsutsugamushi protein OtDUB in complex with Rac1

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

ULP_PROTEASE domain-containing protein

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Ras-related C3 botulinum toxin substrate 1

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

6x1g__assembly_1__model_1

6x1g__assembly_1__model_1 | I(q)

6x1g__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 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (4 domains)

7. Citations (1)