6upu

Crystal structure of the Orientia tsutsugamushi OtDUB in complex with three molecules of ubiquitin

Method: X-RAY DIFFRACTION D_max: 145.9 Å Quality: GOOD

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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 heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain A； UniProt 1–259	Not recorded	Ubiquitin × 3 （F5H388）	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
2	Protein heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain E； UniProt 1–259	Not recorded	Ubiquitin × 3 （F5H388）	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
3	Protein heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain I； UniProt 1–259	Not recorded	Ubiquitin × 3 （F5H388）	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
4	Protein heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain M； UniProt 1–259	Not recorded	Ubiquitin × 3 （F5H388）	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

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 6UPU	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 oligomeric state 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
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
6X1H Crystal structure of a guanine nucleotide exchange factor (GEF) domain from the Orientia tsutsugamushi protein OtDUB Deposited 2020-05-18	Different construct Different oligomeric state 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 oligomeric state 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 oligomeric state 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 oligomeric state 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 oligomeric state 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 oligomeric state 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 9 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 Author chain E； PDBConstruct 2–260； UniProt 1–259 Author chain I； PDBConstruct 2–260； UniProt 1–259 Author chain M； PDBConstruct 2–260； UniProt 1–259

Ubiquitin

Homo sapiens

UniProt F5H388

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 heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain B； UniProt 1–76 Chain C； UniProt 1–76 Chain D； UniProt 1–76	Not recorded	ULP_PROTEASE domain-containing protein × 1 （B3CVM3）	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
2	Protein heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain F； UniProt 1–76 Chain G； UniProt 1–76 Chain H； UniProt 1–76	Not recorded	ULP_PROTEASE domain-containing protein × 1 （B3CVM3）	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
3	Protein heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain J； UniProt 1–76 Chain K； UniProt 1–76 Chain L； UniProt 1–76	Not recorded	ULP_PROTEASE domain-containing protein × 1 （B3CVM3）	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
4	Protein heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain N； UniProt 1–76 Chain O； UniProt 1–76 Chain P； UniProt 1–76	Not recorded	ULP_PROTEASE domain-containing protein × 1 （B3CVM3）	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

Other States of the Same Protein in the Database

Other PDB	Difference from Current Entry 6UPU	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
6NN6 Structure of Dot1L-H2BK120ub nucleosome complex Deposited 2019-01-14	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric	Chain L 75–151（77 aa）	Mutation：G76S	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.90 Å

1 other PDB entries and 1 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	F5H388_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 4–79； UniProt 1–76 Author chain C； PDBConstruct 4–79； UniProt 1–76 Author chain D； PDBConstruct 4–79； UniProt 1–76 Author chain F； PDBConstruct 4–79； UniProt 1–76 Author chain G； PDBConstruct 4–79； UniProt 1–76 Author chain H； PDBConstruct 4–79； UniProt 1–76 Author chain J； PDBConstruct 4–79； UniProt 1–76 Author chain K； PDBConstruct 4–79； UniProt 1–76 Author chain L； PDBConstruct 4–79； UniProt 1–76 Author chain N； PDBConstruct 4–79； UniProt 1–76 Author chain O； PDBConstruct 4–79； UniProt 1–76 Author chain P； PDBConstruct 4–79； UniProt 1–76

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.

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

Download Download SAXS (.dat) P(r) (.pr.out) CIF

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	6upu
Deposition date deposition_date	2019-10-18
Structure title title	Crystal structure of the Orientia tsutsugamushi OtDUB in complex with three molecules of ubiquitin
Keywords keywords	deubiquitylase, Orientia, CE clan, ubiquitin, 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	43.92 Å
Radius of gyration Rg (electron density) rg_electron	43.60 Å
Forward intensity I(0) i0	708018000.00
Molecular weight molecular_weight	218610.0 kDa
Excluded volume excluded_volume	274420 Å³
Envelope volume envelope_volume	387570 Å³
Hydration-shell volume shell_volume	74519 Å³
Envelope diameter envelope_diameter	154.2 Å
Shell Rg shell_rg	48.19 Å
Envelope Rg envelope_rg	43.09 Å
Shape Rg shape_rg	43.60 Å
Total Rg total_rg	43.81 Å
Total atoms total_atoms	15348
Residues n_residues	1948
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	145.9 Å
Rg (real space) rg_real	43.86 Å
Rg uncertainty (real space) rg_real_error	1.13 Å
I(0) (real space) i0_real	7.0800e+08
I(0) uncertainty (real space) i0_real_error	1.2670e+07
Rg (reciprocal space) rg_reciprocal	43.92 Å
I(0) (reciprocal space) i0_reciprocal	708100000.0000
Solution quality estimate total_estimate	0.8780
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	52.7 Å
Skewness Skewness skewness	0.326
Kurtosis Kurtosis kurtosis	-0.250
Angular range angular_range	— – 0.1800 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	61010000.0000
Real-space data points n_real_points	37
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.853; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.998; Smooth: 0.853

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	ULP_PROTEASE domain-containing protein
Molecular weight formula_weight	29222.2 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,E,I,M
Atom count atom_count	15824

GMANDQDLSNPEYLYTEDDINQLLKHYLGLDDRISIIQHVALNESLLLKQTLHQVLSDIFSGMQEKAVIPLHTGNNHWVAMAIKKGMNDDIVISYNDPMGVSIDDKVTLINCIKELCPGAKINDLQTVQQTNVYDCGPFVVDNLIKMSQGQPILSTEEAKQQAQNIRQSQVNFLSENRMITSAAAALADTLLKNNNRITEGVLVDRIFDNKILSVQEKQQLLNNLLDNHIKENKSLTKESLTRMLASTHFVQQQANVLLN

来源 Source

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

Entity 2 Entity 2 polymer

Description description	Ubiquitin
Molecular weight formula_weight	8748.0 kDa
Source method src_method	man
Copy count entity_count	12

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,C,D,F,G,H,J,K,L,N,O,P

GGGMQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	Human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	476

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7. Fold Classification (SCOP + CATH) 33 domains

SCOP 2.08 (19 domains)

Domain ID domain_id	d6upub1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.15 — beta-Grasp (ubiquitin-like)
Superfamily Superfamily superfamily	d.15.1 — Ubiquitin-like
Family Family family	d.15.1.1 — Ubiquitin-related

Domain ID domain_id	d6upub2
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	d6upuc_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.15 — beta-Grasp (ubiquitin-like)
Superfamily Superfamily superfamily	d.15.1 — Ubiquitin-like
Family Family family	d.15.1.1 — Ubiquitin-related

Domain ID domain_id	d6upud_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.15 — beta-Grasp (ubiquitin-like)
Superfamily Superfamily superfamily	d.15.1 — Ubiquitin-like
Family Family family	d.15.1.1 — Ubiquitin-related

Domain ID domain_id	d6upuf1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.15 — beta-Grasp (ubiquitin-like)
Superfamily Superfamily superfamily	d.15.1 — Ubiquitin-like
Family Family family	d.15.1.1 — Ubiquitin-related

Domain ID domain_id	d6upuf2
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	d6upug_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.15 — beta-Grasp (ubiquitin-like)
Superfamily Superfamily superfamily	d.15.1 — Ubiquitin-like
Family Family family	d.15.1.1 — Ubiquitin-related

Domain ID domain_id	d6upuh1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.15 — beta-Grasp (ubiquitin-like)
Superfamily Superfamily superfamily	d.15.1 — Ubiquitin-like
Family Family family	d.15.1.1 — Ubiquitin-related

Domain ID domain_id	d6upuh2
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	d6upuj1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.15 — beta-Grasp (ubiquitin-like)
Superfamily Superfamily superfamily	d.15.1 — Ubiquitin-like
Family Family family	d.15.1.1 — Ubiquitin-related

Domain ID domain_id	d6upuj2
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	d6upuk1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.15 — beta-Grasp (ubiquitin-like)
Superfamily Superfamily superfamily	d.15.1 — Ubiquitin-like
Family Family family	d.15.1.1 — Ubiquitin-related

Domain ID domain_id	d6upuk2
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	d6upul_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.15 — beta-Grasp (ubiquitin-like)
Superfamily Superfamily superfamily	d.15.1 — Ubiquitin-like
Family Family family	d.15.1.1 — Ubiquitin-related

Domain ID domain_id	d6upun1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.15 — beta-Grasp (ubiquitin-like)
Superfamily Superfamily superfamily	d.15.1 — Ubiquitin-like
Family Family family	d.15.1.1 — Ubiquitin-related

Domain ID domain_id	d6upun2
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	d6upuo_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.15 — beta-Grasp (ubiquitin-like)
Superfamily Superfamily superfamily	d.15.1 — Ubiquitin-like
Family Family family	d.15.1.1 — Ubiquitin-related

Domain ID domain_id	d6upup1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.15 — beta-Grasp (ubiquitin-like)
Superfamily Superfamily superfamily	d.15.1 — Ubiquitin-like
Family Family family	d.15.1.1 — Ubiquitin-related

Domain ID domain_id	d6upup2
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 (14 domains)

Domain ID domain_id	6upuB01
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	20 — Ubiquitin-like (UB roll)
Homologous superfamily homologous superfamily	90 — Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1

Domain ID domain_id	6upuC01
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	20 — Ubiquitin-like (UB roll)
Homologous superfamily homologous superfamily	90 — Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1

Domain ID domain_id	6upuD01
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	20 — Ubiquitin-like (UB roll)
Homologous superfamily homologous superfamily	90 — Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1

Domain ID domain_id	6upuE01
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

Domain ID domain_id	6upuF01
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	20 — Ubiquitin-like (UB roll)
Homologous superfamily homologous superfamily	90 — Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1

Domain ID domain_id	6upuG01
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	20 — Ubiquitin-like (UB roll)
Homologous superfamily homologous superfamily	90 — Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1

Domain ID domain_id	6upuH01
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	20 — Ubiquitin-like (UB roll)
Homologous superfamily homologous superfamily	90 — Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1

Domain ID domain_id	6upuJ01
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	20 — Ubiquitin-like (UB roll)
Homologous superfamily homologous superfamily	90 — Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1

Domain ID domain_id	6upuK01
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	20 — Ubiquitin-like (UB roll)
Homologous superfamily homologous superfamily	90 — Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1

Domain ID domain_id	6upuL01
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	20 — Ubiquitin-like (UB roll)
Homologous superfamily homologous superfamily	90 — Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1

Domain ID domain_id	6upuM01
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

Domain ID domain_id	6upuN01
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	20 — Ubiquitin-like (UB roll)
Homologous superfamily homologous superfamily	90 — Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1

Domain ID domain_id	6upuO01
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	20 — Ubiquitin-like (UB roll)
Homologous superfamily homologous superfamily	90 — Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1

Domain ID domain_id	6upuP01
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	20 — Ubiquitin-like (UB roll)
Homologous superfamily homologous superfamily	90 — Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1

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8. Citations (1)

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Unit-cell length a length_a	119.745 Å
Unit-cell length b length_b	144.074 Å
Unit-cell length c length_c	143.474 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	48

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	2.200 Å
Low-resolution limit resolution_low	56.700 Å
R factor r_factor	0.1778
R_work r_work	0.1762
R_free r_free	0.2093

Crystal structure of the Orientia tsutsugamushi OtDUB in complex with three molecules of ubiquitin

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

Ubiquitin

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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 water

7. Fold Classification (SCOP + CATH) 33 domains

SCOP 2.08 (19 domains)

CATH v4.4 (14 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)

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