SAXSdb — 6x1h

▼

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

ULP_PROTEASE domain-containing protein

Orientia tsutsugamushi

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain E； UniProt 548–759	Not recorded	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：MICROBATCH；pH 7；293 K；2.4 M sodium malonate pH 7.0	Resolution 2.91 Å R-free 0.208
2	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain D； UniProt 548–759	Not recorded	NI NICKEL (II) ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：MICROBATCH；pH 7；293 K；2.4 M sodium malonate pH 7.0	Resolution 2.91 Å R-free 0.208
3	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain B； UniProt 548–759	Not recorded	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：MICROBATCH；pH 7；293 K；2.4 M sodium malonate pH 7.0	Resolution 2.91 Å R-free 0.208
4	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain F； UniProt 548–759	Not recorded	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：MICROBATCH；pH 7；293 K；2.4 M sodium malonate pH 7.0	Resolution 2.91 Å R-free 0.208
5	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain C； UniProt 548–759	Not recorded	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：MICROBATCH；pH 7；293 K；2.4 M sodium malonate pH 7.0	Resolution 2.91 Å R-free 0.208
6	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 548–759	Not recorded	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：MICROBATCH；pH 7；293 K；2.4 M sodium malonate pH 7.0	Resolution 2.91 Å R-free 0.208

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 6X1H	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
6UPS Crystal structure of the deubiquitylase domain from the Orientia tsutsugamushi protein OTT_1962 (OtDUB) Deposited 2019-10-18	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–259（259 aa） Fragment：deubiquitylase domain	Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；298 K；0.2 M ammonium iodide, 20% (w/v) PEG 3350	Resolution 2.00 Å R-free 0.237
6UPU Crystal structure of the Orientia tsutsugamushi OtDUB in complex with three molecules of ubiquitin Deposited 2019-10-18	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 1–259（259 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions MICROBATCH；pH 7.5；298 K；150 mM potassium thiocyanate, 32.5% (w/v) PEG 3350	Resolution 2.20 Å R-free 0.209
6UPU Crystal structure of the Orientia tsutsugamushi OtDUB in complex with three molecules of ubiquitin Deposited 2019-10-18	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain E 1–259（259 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions MICROBATCH；pH 7.5；298 K；150 mM potassium thiocyanate, 32.5% (w/v) PEG 3350	Resolution 2.20 Å R-free 0.209
6UPU Crystal structure of the Orientia tsutsugamushi OtDUB in complex with three molecules of ubiquitin Deposited 2019-10-18	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain I 1–259（259 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions MICROBATCH；pH 7.5；298 K；150 mM potassium thiocyanate, 32.5% (w/v) PEG 3350	Resolution 2.20 Å R-free 0.209
6UPU Crystal structure of the Orientia tsutsugamushi OtDUB in complex with three molecules of ubiquitin Deposited 2019-10-18	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain M 1–259（259 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions MICROBATCH；pH 7.5；298 K；150 mM potassium thiocyanate, 32.5% (w/v) PEG 3350	Resolution 2.20 Å R-free 0.209
6X1G Crystal structure of a GEF domain from the Orientia tsutsugamushi protein OtDUB in complex with Rac1 Deposited 2020-05-18	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 548–759（212 aa） Fragment：GEF domain	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions MICROBATCH；pH 9.5；293 K；25 mM CHES pH 9.5, 25% (w/v) PEG 8000	Resolution 1.60 Å R-free 0.218
6X1G Crystal structure of a GEF domain from the Orientia tsutsugamushi protein OtDUB in complex with Rac1 Deposited 2020-05-18	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 548–759（212 aa） Fragment：GEF domain	Not recorded	MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions MICROBATCH；pH 9.5；293 K；25 mM CHES pH 9.5, 25% (w/v) PEG 8000	Resolution 1.60 Å R-free 0.218

3 other PDB entries and 7 assemblies. Open the comparison page and filter oligomeric states

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 B； PDBConstruct 2–213； UniProt 548–759 Author chain C； PDBConstruct 2–213； UniProt 548–759 Author chain D； PDBConstruct 2–213； UniProt 548–759 Author chain E； PDBConstruct 2–213； UniProt 548–759 Author chain F； PDBConstruct 2–213； UniProt 548–759

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	6x1h
Deposition date deposition_date	2020-05-18
Structure title title	Crystal structure of a guanine nucleotide exchange factor (GEF) domain from the Orientia tsutsugamushi protein OtDUB
Keywords keywords	guanine nucleotide exchange factor, GEF, Orientia tsutsugamushi, scrub typhus, SIGNALING PROTEIN; SIGNALING PROTEIN
Experimental Method method	X-RAY DIFFRACTION

▼

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	46.60 Å
Radius of gyration Rg (electron density) rg_electron	46.88 Å
Forward intensity I(0) i0	317330000.00
Molecular weight molecular_weight	146110.0 kDa
Excluded volume excluded_volume	183250 Å³
Envelope volume envelope_volume	289470 Å³
Hydration-shell volume shell_volume	54906 Å³
Envelope diameter envelope_diameter	174.7 Å
Shell Rg shell_rg	47.23 Å
Envelope Rg envelope_rg	45.93 Å
Shape Rg shape_rg	46.89 Å
Total Rg total_rg	46.88 Å
Total atoms total_atoms	10289
Residues n_residues	1279
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

▼

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	166.4 Å
Rg (real space) rg_real	47.00 Å
Rg uncertainty (real space) rg_real_error	2.15 Å
I(0) (real space) i0_real	3.1730e+08
I(0) uncertainty (real space) i0_real_error	7.0600e+06
Rg (reciprocal space) rg_reciprocal	46.60 Å
I(0) (reciprocal space) i0_reciprocal	317200000.0000
Solution quality estimate total_estimate	0.6362
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	49.0 Å
Skewness Skewness skewness	0.529
Kurtosis Kurtosis kurtosis	-0.208
Angular range angular_range	— – 0.1700 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	19760000.0000
Real-space data points n_real_points	35
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.732; Stabil: 1.000; Sysdev: 0.115; Positv: 1.000; Valcen: 0.962; Smooth: 0.763

▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (3)

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	6

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	E,D,B,F,C,A
Atom count atom_count	10290

MERLVKKVTSNLETELKFFKGRLVQELMQIVKNENGRIDHTSKNWQESASVLLNSQEKGAVSLAEVERAVSKMTQKLRDQKVSEEEVVNIESKLKFERASLEAKLFDDNEIKELINKRIKEDALRAIPFLGSDSESFMEKISPFVKLPDDSYSLLKANDKHHPFQNILYSNALKFFADSSDIGYLNDDSLKNLTPENLNAFEQAVAADIDKLMHHHHHH

来源 Source

来源生物 organism	Orientia tsutsugamushi
通用名 common_name	Rickettsia tsutsugamushi
NCBI Class编号 ncbi_taxonomy_id	334380
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	NICKEL (II) ION
Molecular weight formula_weight	58.7 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	1

▶

8. Citations (1)

▶

Unit-cell length a length_a	110.533 Å
Unit-cell length b length_b	110.533 Å
Unit-cell length c length_c	251.240 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	36

Space group space_group	P 63
Space-group number int_tables_number	173
Crystal system crystal_system	—

Resolution resolution	2.910 Å
Low-resolution limit resolution_low	47.860 Å
R factor r_factor	0.1683
R_work r_work	0.1663
R_free r_free	0.2082

fit	/app/data/saxs_computation/x1/6x1h/6x1h.fit
pddf	/app/data/pr_computation/x1/6x1h/6x1h.pr.out
profile	/app/data/saxs_computation/x1/6x1h/6x1h.dat

Crystal structure of a guanine nucleotide exchange factor (GEF) domain from the Orientia tsutsugamushi protein OtDUB

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

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction