SAXSdb — 6ups

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

ULP_PROTEASE domain-containing protein

Orientia tsutsugamushi (strain Ikeda)

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 A； UniProt 1–259	Fragment：deubiquitylase domain Non-standard monomer：Yes (specific site not provided by mmCIF)	No other associated polymer	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

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 6UPS	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
6UPU Crystal structure of the Orientia tsutsugamushi OtDUB in complex with three molecules of ubiquitin Deposited 2019-10-18	Different construct Different mutation/modification 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 mutation/modification 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 mutation/modification 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 mutation/modification 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 mutation/modification 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 mutation/modification 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
6X1H Crystal structure of a guanine nucleotide exchange factor (GEF) domain from the Orientia tsutsugamushi protein OtDUB Deposited 2020-05-18	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain E 548–759（212 aa）	Not recorded	No recorded non-water small molecule	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
6X1H Crystal structure of a guanine nucleotide exchange factor (GEF) domain from the Orientia tsutsugamushi protein OtDUB Deposited 2020-05-18	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain D 548–759（212 aa）	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
6X1H Crystal structure of a guanine nucleotide exchange factor (GEF) domain from the Orientia tsutsugamushi protein OtDUB Deposited 2020-05-18	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 548–759（212 aa）	Not recorded	No recorded non-water small molecule	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
6X1H Crystal structure of a guanine nucleotide exchange factor (GEF) domain from the Orientia tsutsugamushi protein OtDUB Deposited 2020-05-18	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain F 548–759（212 aa）	Not recorded	No recorded non-water small molecule	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
6X1H Crystal structure of a guanine nucleotide exchange factor (GEF) domain from the Orientia tsutsugamushi protein OtDUB Deposited 2020-05-18	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 5 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain C 548–759（212 aa）	Not recorded	No recorded non-water small molecule	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
6X1H Crystal structure of a guanine nucleotide exchange factor (GEF) domain from the Orientia tsutsugamushi protein OtDUB Deposited 2020-05-18	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 6 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 548–759（212 aa）	Not recorded	No recorded non-water small molecule	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 other PDB entries and 12 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 2–260； UniProt 1–259

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	6ups
Deposition date deposition_date	2019-10-18
Structure title title	Crystal structure of the deubiquitylase domain from the Orientia tsutsugamushi protein OTT_1962 (OtDUB)
Keywords keywords	deubiquitylase, Orientia, CE clan, HYDROLASE; HYDROLASE
Experimental Method method	X-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier	22.13 Å
Radius of gyration Rg (electron density) rg_electron	21.52 Å
Forward intensity I(0) i0	14201900.00
Molecular weight molecular_weight	27794.0 kDa
Excluded volume excluded_volume	34491 Å³
Envelope volume envelope_volume	42999 Å³
Hydration-shell volume shell_volume	17633 Å³
Envelope diameter envelope_diameter	71.5 Å
Shell Rg shell_rg	27.12 Å
Envelope Rg envelope_rg	21.61 Å
Shape Rg shape_rg	21.50 Å
Total Rg total_rg	22.35 Å
Total atoms total_atoms	1925
Residues n_residues	238
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

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

Maximum dimension Dmax dmax	71.3 Å
Rg (real space) rg_real	22.20 Å
Rg uncertainty (real space) rg_real_error	0.51 Å
I(0) (real space) i0_real	1.4200e+07
I(0) uncertainty (real space) i0_real_error	2.0380e+05
Rg (reciprocal space) rg_reciprocal	22.19 Å
I(0) (reciprocal space) i0_reciprocal	14200000.0000
Solution quality estimate total_estimate	0.8917
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	21.3 Å
Skewness Skewness skewness	0.349
Kurtosis Kurtosis kurtosis	-0.542
Angular range angular_range	— – 0.3600 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	3251000.0000
Real-space data points n_real_points	68
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.896; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.911; Smooth: 0.989

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

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7. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

Domain ID domain_id	6upsA01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	395 — Adenoviral Proteinase; Chain
Homologous superfamily homologous superfamily	10 — Adenoviral Proteinase; Chain A

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8. Citations (1)

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Unit-cell length a length_a	114.787 Å
Unit-cell length b length_b	43.093 Å
Unit-cell length c length_c	58.244 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	4

Space group space_group	P 21 21 2
Space-group number int_tables_number	18
Crystal system crystal_system	—

Resolution resolution	2.000 Å
Low-resolution limit resolution_low	34.670 Å
R factor r_factor	0.2092
R_work r_work	0.2077
R_free r_free	0.2371

Description description	ULP_PROTEASE domain-containing protein
Molecular weight formula_weight	29597.4 kDa
EC 编号 ec_number	3.4.22.-
Source method src_method	man
Copy count entity_count	1

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	2005

Crystal structure of the deubiquitylase domain from the Orientia tsutsugamushi protein OTT_1962 (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

6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 water

7. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)

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

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	80

fit	/app/data/saxs_computation/up/6ups/6ups.fit
pddf	/app/data/pr_computation/up/6ups/6ups.pr.out
profile	/app/data/saxs_computation/up/6ups/6ups.dat