PDB-6upu: Crystal structure of the Orientia tsutsugamushi OtDUB in complex ...

ID or keywords:

Entry

Database: PDB / ID: 6upu

Title

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

Components

ULP_PROTEASE domain-containing protein
Ubiquitin

Keywords

HYDROLASE / deubiquitylase / Orientia / CE clan / ubiquitin

Function / homology

Function and homology information

cysteine-type peptidase activity / Maturation of protein E / Maturation of protein E / ER Quality Control Compartment (ERQC) / Myoclonic epilepsy of Lafora / FLT3 signaling by CBL mutants / Prevention of phagosomal-lysosomal fusion / IRAK2 mediated activation of TAK1 complex / Alpha-protein kinase 1 signaling pathway / Glycogen synthesis ...cysteine-type peptidase activity / Maturation of protein E / Maturation of protein E / ER Quality Control Compartment (ERQC) / Myoclonic epilepsy of Lafora / FLT3 signaling by CBL mutants / Prevention of phagosomal-lysosomal fusion / IRAK2 mediated activation of TAK1 complex / Alpha-protein kinase 1 signaling pathway / Glycogen synthesis / IRAK1 recruits IKK complex / IRAK1 recruits IKK complex upon TLR7/8 or 9 stimulation / Membrane binding and targetting of GAG proteins / Endosomal Sorting Complex Required For Transport (ESCRT) / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / Negative regulation of FLT3 / Constitutive Signaling by NOTCH1 HD Domain Mutants / Regulation of FZD by ubiquitination / TICAM1,TRAF6-dependent induction of TAK1 complex / NOTCH2 Activation and Transmission of Signal to the Nucleus / TICAM1-dependent activation of IRF3/IRF7 / APC/C:Cdc20 mediated degradation of Cyclin B / p75NTR recruits signalling complexes / Downregulation of ERBB4 signaling / APC-Cdc20 mediated degradation of Nek2A / PINK1-PRKN Mediated Mitophagy / TRAF6-mediated induction of TAK1 complex within TLR4 complex / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / Pexophagy / Regulation of innate immune responses to cytosolic DNA / InlA-mediated entry of Listeria monocytogenes into host cells / VLDLR internalisation and degradation / Downregulation of ERBB2:ERBB3 signaling / NF-kB is activated and signals survival / NRIF signals cell death from the nucleus / Regulation of PTEN localization / Activated NOTCH1 Transmits Signal to the Nucleus / Regulation of BACH1 activity / Translesion synthesis by REV1 / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / Translesion synthesis by POLK / MAP3K8 (TPL2)-dependent MAPK1/3 activation / TICAM1, RIP1-mediated IKK complex recruitment / Downregulation of TGF-beta receptor signaling / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / Translesion synthesis by POLI / Gap-filling DNA repair synthesis and ligation in GG-NER / Josephin domain DUBs / Regulation of activated PAK-2p34 by proteasome mediated degradation / InlB-mediated entry of Listeria monocytogenes into host cell / IKK complex recruitment mediated by RIP1 / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / Autodegradation of Cdh1 by Cdh1:APC/C / TNFR1-induced NF-kappa-B signaling pathway / APC/C:Cdc20 mediated degradation of Securin / Asymmetric localization of PCP proteins / TCF dependent signaling in response to WNT / SCF-beta-TrCP mediated degradation of Emi1 / NIK-->noncanonical NF-kB signaling / Ubiquitin-dependent degradation of Cyclin D / Regulation of NF-kappa B signaling / AUF1 (hnRNP D0) binds and destabilizes mRNA / TNFR2 non-canonical NF-kB pathway / activated TAK1 mediates p38 MAPK activation / Assembly of the pre-replicative complex / Vpu mediated degradation of CD4 / NOTCH3 Activation and Transmission of Signal to the Nucleus / Negative regulators of DDX58/IFIH1 signaling / Deactivation of the beta-catenin transactivating complex / Degradation of DVL / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / Regulation of signaling by CBL / Dectin-1 mediated noncanonical NF-kB signaling / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / Fanconi Anemia Pathway / Hh mutants are degraded by ERAD / Recognition of DNA damage by PCNA-containing replication complex / Negative regulation of FGFR3 signaling / Peroxisomal protein import / Degradation of AXIN / Degradation of GLI1 by the proteasome / Downregulation of SMAD2/3:SMAD4 transcriptional activity / Activation of NF-kappaB in B cells / Regulation of TNFR1 signaling / Termination of translesion DNA synthesis / Negative regulation of FGFR2 signaling / Hedgehog ligand biogenesis / Defective CFTR causes cystic fibrosis / Stabilization of p53 / EGFR downregulation / Negative regulation of FGFR4 signaling / Negative regulation of NOTCH4 signaling / Iron uptake and transport / GSK3B and BTRC:CUL1-mediated-degradation of NFE2L2 / Negative regulation of FGFR1 signaling / G2/M Checkpoints / SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription
Similarity search - Function

Biological species

Orientia tsutsugamushi (bacteria)

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.2 Å

Authors

Lim, C.S. / Ronau, J.A. / Xiong, Y.

Funding support

United States, 3items

Organization	Grant number	Country
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	R01-AI116313	United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	R01-GM046904	United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	R01-GM053756	United States

Citation

Journal: Nat Commun / Year: 2020
Title: A deubiquitylase with an unusually high-affinity ubiquitin-binding domain from the scrub typhus pathogen Orientia tsutsugamushi.
Authors: Berk, J.M. / Lim, C. / Ronau, J.A. / Chaudhuri, A. / Chen, H. / Beckmann, J.F. / Loria, J.P. / Xiong, Y. / Hochstrasser, M.

History

Deposition	Oct 18, 2019	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Apr 1, 2020	Provider: repository / Type: Initial release
Revision 1.1	Apr 14, 2021	Group: Database references / Category: citation / citation_author Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2	Mar 13, 2024	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.3	Apr 3, 2024	Group: Refinement description / Category: pdbx_initial_refinement_model

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	6upu.cif.gz	779.9 KB	Display	PDBx/mmCIF format
PDB format	pdb6upu.ent.gz	650 KB	Display	PDB format
PDBx/mmJSON format	6upu.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	6upu_validation.pdf.gz	540.5 KB	Display	wwPDB validaton report
Full document	6upu_full_validation.pdf.gz	593.3 KB	Display
Data in XML	6upu_validation.xml.gz	74 KB	Display
Data in CIF	6upu_validation.cif.gz	103.9 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/up/6upu ftp://data.pdbj.org/pub/pdb/validation_reports/up/6upu	HTTPS FTP

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Related structure data

Related structure data	6upsC C: citing same article (ref.)
Similar structure data	1jec-d 4j0u-d 6kr1-4 1ydm-d 6kr1-3 5mfc-1 6kr1-1 5jmc-1 6nt2-2 2ziw-d Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

Related structure data

6upsC

C: citing same article (ref.)

Similar structure data

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#60 - Dec 2004 Ubiquitin similarity (68) #234 - Jun 2019 MDM2 and Cancer similarity (66) #122 - Feb 2010 Enhanceosome similarity (6) #88 - Apr 2007 Clathrin similarity (1) #150 - Jun 2012 Sliding Clamps similarity (5) #172 - Apr 2014 RecA and Rad51 similarity (8) #68 - Aug 2005 Neurotrophins similarity (3) #143 - Nov 2011 Toll-like Receptors similarity (4) #56 - Aug 2004 Caspases similarity (3) #255 - Mar 2021 Cisplatin and DNA similarity (2) #126 - Jun 2010 Epidermal Growth Factor similarity (1) #43 - Jul 2003 Src Tyrosine Kinase similarity (2) #195 - Mar 2016 RAF Protein Kinases similarity (1) #205 - Jan 2017 Nuclear Pore Complex similarity (1) #163 - Jul 2013 HIV Capsid similarity (1) #266 - Feb 2022 Oligosaccharyltransferase similarity (1) #112 - Apr 2009 Oct and Sox Transcription Factors similarity (1)

PDB pages

PDBj /

wwPDB /

NCBI

Related items in Molecule of the Month

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Deposited unit

A: ULP_PROTEASE domain-containing protein

B: Ubiquitin

C: Ubiquitin

D: Ubiquitin

E: ULP_PROTEASE domain-containing protein

F: Ubiquitin

G: Ubiquitin

H: Ubiquitin

I: ULP_PROTEASE domain-containing protein

J: Ubiquitin

K: Ubiquitin

L: Ubiquitin

M: ULP_PROTEASE domain-containing protein

N: Ubiquitin

O: Ubiquitin

P: Ubiquitin

222 kDa, 16 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: ULP_PROTEASE domain-containing protein

B: Ubiquitin

C: Ubiquitin

D: Ubiquitin

defined by author
Evidence: gel filtration, Two dimers per asymmetric unit; 4 total OtDUB chains, with 3 ubiquitins bound to each OtDUB (12 total)
55.5 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

E: ULP_PROTEASE domain-containing protein

F: Ubiquitin

G: Ubiquitin

H: Ubiquitin

defined by author
55.5 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

I: ULP_PROTEASE domain-containing protein

J: Ubiquitin

K: Ubiquitin

L: Ubiquitin

defined by author
55.5 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

4

M: ULP_PROTEASE domain-containing protein

N: Ubiquitin

O: Ubiquitin

P: Ubiquitin

defined by author
55.5 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	119.745, 144.074, 143.474
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁

Noncrystallographic symmetry (NCS)

NCS domain:
NCS domain segments:

Component-ID: _ / Refine code: _

Dom-ID	Ens-ID	Beg auth comp-ID	Beg label comp-ID	End auth comp-ID	End label comp-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	ALA	ALA	LEU	LEU	A	A	2 - 258	3 - 259
2	1	ALA	ALA	LEU	LEU	E	E	2 - 258	3 - 259
1	2	ALA	ALA	LEU	LEU	A	A	2 - 258	3 - 259
2	2	ALA	ALA	LEU	LEU	I	I	2 - 258	3 - 259
1	3	ALA	ALA	LEU	LEU	A	A	2 - 258	3 - 259
2	3	ALA	ALA	LEU	LEU	M	M	2 - 258	3 - 259
1	4	MET	MET	GLY	GLY	B	B	1 - 75	4 - 78
2	4	MET	MET	GLY	GLY	C	C	1 - 75	4 - 78
1	5	MET	MET	GLY	GLY	B	B	1 - 75	4 - 78
2	5	MET	MET	GLY	GLY	D	D	1 - 75	4 - 78
1	6	GLY	GLY	GLY	GLY	B	B	0 - 76	3 - 79
2	6	GLY	GLY	GLY	GLY	F	F	0 - 76	3 - 79
1	7	MET	MET	ARG	ARG	B	B	1 - 74	4 - 77
2	7	MET	MET	ARG	ARG	G	G	1 - 74	4 - 77
1	8	GLY	GLY	ARG	ARG	B	B	0 - 74	3 - 77
2	8	GLY	GLY	ARG	ARG	H	H	0 - 74	3 - 77
1	9	GLY	GLY	GLY	GLY	B	B	0 - 76	3 - 79
2	9	GLY	GLY	GLY	GLY	J	J	0 - 76	3 - 79
1	10	GLY	GLY	LEU	LEU	B	B	0 - 73	3 - 76
2	10	GLY	GLY	LEU	LEU	K	K	0 - 73	3 - 76
1	11	MET	MET	GLY	GLY	B	B	1 - 75	4 - 78
2	11	MET	MET	GLY	GLY	L	L	1 - 75	4 - 78
1	12	GLY	GLY	GLY	GLY	B	B	0 - 75	3 - 78
2	12	GLY	GLY	GLY	GLY	N	N	0 - 75	3 - 78
1	13	MET	MET	ARG	ARG	B	B	1 - 74	4 - 77
2	13	MET	MET	ARG	ARG	O	O	1 - 74	4 - 77
1	14	GLY	GLY	GLY	GLY	B	B	0 - 76	3 - 79
2	14	GLY	GLY	GLY	GLY	P	P	0 - 76	3 - 79
1	15	MET	MET	GLY	GLY	C	C	1 - 76	4 - 79
2	15	MET	MET	GLY	GLY	D	D	1 - 76	4 - 79
1	16	MET	MET	GLY	GLY	C	C	1 - 75	4 - 78
2	16	MET	MET	GLY	GLY	F	F	1 - 75	4 - 78
1	17	MET	MET	ARG	ARG	C	C	1 - 74	4 - 77
2	17	MET	MET	ARG	ARG	G	G	1 - 74	4 - 77
1	18	MET	MET	ARG	ARG	C	C	1 - 74	4 - 77
2	18	MET	MET	ARG	ARG	H	H	1 - 74	4 - 77
1	19	MET	MET	GLY	GLY	C	C	1 - 75	4 - 78
2	19	MET	MET	GLY	GLY	J	J	1 - 75	4 - 78
1	20	MET	MET	LEU	LEU	C	C	1 - 73	4 - 76
2	20	MET	MET	LEU	LEU	K	K	1 - 73	4 - 76
1	21	MET	MET	GLY	GLY	C	C	1 - 76	4 - 79
2	21	MET	MET	GLY	GLY	L	L	1 - 76	4 - 79
1	22	MET	MET	GLY	GLY	C	C	1 - 75	4 - 78
2	22	MET	MET	GLY	GLY	N	N	1 - 75	4 - 78
1	23	MET	MET	ARG	ARG	C	C	1 - 74	4 - 77
2	23	MET	MET	ARG	ARG	O	O	1 - 74	4 - 77
1	24	MET	MET	GLY	GLY	C	C	1 - 75	4 - 78
2	24	MET	MET	GLY	GLY	P	P	1 - 75	4 - 78
1	25	MET	MET	GLY	GLY	D	D	1 - 75	4 - 78
2	25	MET	MET	GLY	GLY	F	F	1 - 75	4 - 78
1	26	MET	MET	ARG	ARG	D	D	1 - 74	4 - 77
2	26	MET	MET	ARG	ARG	G	G	1 - 74	4 - 77
1	27	MET	MET	ARG	ARG	D	D	1 - 74	4 - 77
2	27	MET	MET	ARG	ARG	H	H	1 - 74	4 - 77
1	28	MET	MET	GLY	GLY	D	D	1 - 75	4 - 78
2	28	MET	MET	GLY	GLY	J	J	1 - 75	4 - 78
1	29	MET	MET	LEU	LEU	D	D	1 - 73	4 - 76
2	29	MET	MET	LEU	LEU	K	K	1 - 73	4 - 76
1	30	MET	MET	GLY	GLY	D	D	1 - 76	4 - 79
2	30	MET	MET	GLY	GLY	L	L	1 - 76	4 - 79
1	31	MET	MET	GLY	GLY	D	D	1 - 75	4 - 78
2	31	MET	MET	GLY	GLY	N	N	1 - 75	4 - 78
1	32	MET	MET	ARG	ARG	D	D	1 - 74	4 - 77
2	32	MET	MET	ARG	ARG	O	O	1 - 74	4 - 77
1	33	MET	MET	GLY	GLY	D	D	1 - 75	4 - 78
2	33	MET	MET	GLY	GLY	P	P	1 - 75	4 - 78
1	34	ALA	ALA	ASN	ASN	E	E	2 - 259	3 - 260
2	34	ALA	ALA	ASN	ASN	I	I	2 - 259	3 - 260
1	35	ALA	ALA	ASN	ASN	E	E	2 - 259	3 - 260
2	35	ALA	ALA	ASN	ASN	M	M	2 - 259	3 - 260
1	36	MET	MET	ARG	ARG	F	F	1 - 74	4 - 77
2	36	MET	MET	ARG	ARG	G	G	1 - 74	4 - 77
1	37	GLY	GLY	ARG	ARG	F	F	0 - 74	3 - 77
2	37	GLY	GLY	ARG	ARG	H	H	0 - 74	3 - 77
1	38	GLY	GLY	GLY	GLY	F	F	0 - 76	3 - 79
2	38	GLY	GLY	GLY	GLY	J	J	0 - 76	3 - 79
1	39	GLY	GLY	LEU	LEU	F	F	0 - 73	3 - 76
2	39	GLY	GLY	LEU	LEU	K	K	0 - 73	3 - 76
1	40	MET	MET	GLY	GLY	F	F	1 - 75	4 - 78
2	40	MET	MET	GLY	GLY	L	L	1 - 75	4 - 78
1	41	GLY	GLY	GLY	GLY	F	F	0 - 75	3 - 78
2	41	GLY	GLY	GLY	GLY	N	N	0 - 75	3 - 78
1	42	MET	MET	ARG	ARG	F	F	1 - 74	4 - 77
2	42	MET	MET	ARG	ARG	O	O	1 - 74	4 - 77
1	43	GLY	GLY	GLY	GLY	F	F	0 - 76	3 - 79
2	43	GLY	GLY	GLY	GLY	P	P	0 - 76	3 - 79
1	44	MET	MET	ARG	ARG	G	G	1 - 74	4 - 77
2	44	MET	MET	ARG	ARG	H	H	1 - 74	4 - 77
1	45	MET	MET	ARG	ARG	G	G	1 - 74	4 - 77
2	45	MET	MET	ARG	ARG	J	J	1 - 74	4 - 77
1	46	MET	MET	LEU	LEU	G	G	1 - 73	4 - 76
2	46	MET	MET	LEU	LEU	K	K	1 - 73	4 - 76
1	47	MET	MET	ARG	ARG	G	G	1 - 74	4 - 77
2	47	MET	MET	ARG	ARG	L	L	1 - 74	4 - 77
1	48	MET	MET	ARG	ARG	G	G	1 - 74	4 - 77
2	48	MET	MET	ARG	ARG	N	N	1 - 74	4 - 77
1	49	MET	MET	GLY	GLY	G	G	1 - 75	4 - 78
2	49	MET	MET	GLY	GLY	O	O	1 - 75	4 - 78
1	50	MET	MET	ARG	ARG	G	G	1 - 74	4 - 77
2	50	MET	MET	ARG	ARG	P	P	1 - 74	4 - 77
1	51	GLY	GLY	ARG	ARG	H	H	0 - 74	3 - 77
2	51	GLY	GLY	ARG	ARG	J	J	0 - 74	3 - 77
1	52	GLY	GLY	LEU	LEU	H	H	0 - 73	3 - 76
2	52	GLY	GLY	LEU	LEU	K	K	0 - 73	3 - 76
1	53	MET	MET	ARG	ARG	H	H	1 - 74	4 - 77
2	53	MET	MET	ARG	ARG	L	L	1 - 74	4 - 77
1	54	GLY	GLY	ARG	ARG	H	H	0 - 74	3 - 77
2	54	GLY	GLY	ARG	ARG	N	N	0 - 74	3 - 77
1	55	MET	MET	ARG	ARG	H	H	1 - 74	4 - 77
2	55	MET	MET	ARG	ARG	O	O	1 - 74	4 - 77
1	56	GLY	GLY	ARG	ARG	H	H	0 - 74	3 - 77
2	56	GLY	GLY	ARG	ARG	P	P	0 - 74	3 - 77
1	57	ALA	ALA	ASN	ASN	I	I	2 - 259	3 - 260
2	57	ALA	ALA	ASN	ASN	M	M	2 - 259	3 - 260
1	58	GLY	GLY	LEU	LEU	J	J	0 - 73	3 - 76
2	58	GLY	GLY	LEU	LEU	K	K	0 - 73	3 - 76
1	59	MET	MET	GLY	GLY	J	J	1 - 75	4 - 78
2	59	MET	MET	GLY	GLY	L	L	1 - 75	4 - 78
1	60	GLY	GLY	GLY	GLY	J	J	0 - 75	3 - 78
2	60	GLY	GLY	GLY	GLY	N	N	0 - 75	3 - 78
1	61	MET	MET	ARG	ARG	J	J	1 - 74	4 - 77
2	61	MET	MET	ARG	ARG	O	O	1 - 74	4 - 77
1	62	GLY	GLY	GLY	GLY	J	J	0 - 76	3 - 79
2	62	GLY	GLY	GLY	GLY	P	P	0 - 76	3 - 79
1	63	MET	MET	LEU	LEU	K	K	1 - 73	4 - 76
2	63	MET	MET	LEU	LEU	L	L	1 - 73	4 - 76
1	64	GLY	GLY	LEU	LEU	K	K	0 - 73	3 - 76
2	64	GLY	GLY	LEU	LEU	N	N	0 - 73	3 - 76
1	65	MET	MET	LEU	LEU	K	K	1 - 73	4 - 76
2	65	MET	MET	LEU	LEU	O	O	1 - 73	4 - 76
1	66	GLY	GLY	LEU	LEU	K	K	0 - 73	3 - 76
2	66	GLY	GLY	LEU	LEU	P	P	0 - 73	3 - 76
1	67	MET	MET	GLY	GLY	L	L	1 - 75	4 - 78
2	67	MET	MET	GLY	GLY	N	N	1 - 75	4 - 78
1	68	MET	MET	ARG	ARG	L	L	1 - 74	4 - 77
2	68	MET	MET	ARG	ARG	O	O	1 - 74	4 - 77
1	69	MET	MET	GLY	GLY	L	L	1 - 75	4 - 78
2	69	MET	MET	GLY	GLY	P	P	1 - 75	4 - 78
1	70	MET	MET	ARG	ARG	N	N	1 - 74	4 - 77
2	70	MET	MET	ARG	ARG	O	O	1 - 74	4 - 77
1	71	GLY	GLY	GLY	GLY	N	N	0 - 75	3 - 78
2	71	GLY	GLY	GLY	GLY	P	P	0 - 75	3 - 78
1	72	MET	MET	ARG	ARG	O	O	1 - 74	4 - 77
2	72	MET	MET	ARG	ARG	P	P	1 - 74	4 - 77

NCS ensembles :

#1: Protein	ULP_PROTEASE domain-containing protein / DUB Mass: 29222.207 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Orientia tsutsugamushi (strain Ikeda) (bacteria) Strain: Ikeda / Gene: OTT_1962 / Production host: Escherichia coli (E. coli) / References: UniProt: B3CVM3
#2: Protein	Ubiquitin Mass: 8747.986 Da / Num. of mol.: 12 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: UBC / Production host: Escherichia coli (E. coli) / References: UniProt: F5H388, UniProt: P0CG48*PLUS
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 476 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.81 Å³/Da / Density % sol: 56.24 %
Crystal grow	Temperature: 298 K / Method: microbatch / pH: 7.5 / Details: 150 mM potassium thiocyanate, 32.5% (w/v) PEG 3350

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Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 24-ID-E / Wavelength: 0.98 Å

Detector

Type: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 12, 2019

Radiation

Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.98 Å / Relative weight: 1

Reflection twin

Crystal-ID	ID	Operator	Domain-ID	Fraction
1	1	H, K, L	1	0.742
1	1	-H, -L, -K	2	0.258

Reflection

Resolution: 2.2→70 Å / Num. obs: 121784 / % possible obs: 97.5 % / Redundancy: 3.6 % / R_merge(I) obs: 0.102 / R_pim(I) all: 0.06 / R_rim(I) all: 0.119 / Χ²: 1.101 / Net I/σ(I): 9.5 / Num. measured all: 435082

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique obs	CC_1/2	R_pim(I) all	R_rim(I) all	Χ²	% possible all
2.2-2.24	3.2	0.696	6091	0.395	0.452	0.835	0.877	99
2.24-2.28	3.2	0.641	6114	0.47	0.417	0.77	0.89	99
2.28-2.32	3.2	0.594	6151	0.51	0.384	0.712	0.878	99.2
2.32-2.37	3.2	0.547	6063	0.557	0.353	0.655	0.891	99
2.37-2.42	3.1	0.488	6175	0.621	0.317	0.586	0.871	98.8
2.42-2.48	3.1	0.449	6029	0.664	0.293	0.539	0.912	97.7
2.48-2.54	3	0.395	6014	0.697	0.261	0.476	0.91	97.4
2.54-2.61	2.9	0.355	6025	0.73	0.237	0.43	0.912	96.8
2.61-2.69	2.8	0.284	5660	0.822	0.189	0.343	0.976	92.2
2.69-2.77	3.3	0.253	5917	0.877	0.158	0.3	0.973	94.7
2.77-2.87	3.7	0.219	6060	0.925	0.128	0.254	1.08	97.3
2.87-2.99	3.9	0.187	6005	0.946	0.106	0.216	1.126	96.9
2.99-3.12	4	0.151	6004	0.964	0.085	0.174	1.174	96.2
3.12-3.29	4	0.12	6092	0.975	0.067	0.138	1.339	98.2
3.29-3.49	4	0.086	6231	0.987	0.048	0.1	1.406	99.2
3.49-3.76	3.9	0.071	6196	0.99	0.04	0.082	1.49	98.8
3.76-4.14	3.8	0.059	5864	0.993	0.032	0.068	1.512	93.3
4.14-4.74	4.6	0.051	6316	0.995	0.026	0.057	1.21	100
4.74-5.97	4.4	0.048	6367	0.996	0.025	0.054	1.088	99.6
5.97-70	4	0.035	6410	0.998	0.018	0.039	0.961	96.7

-
Processing

Software

Name	Version	Classification
REFMAC	5.8.0238	refinement
HKL-2000		data scaling
PDB_EXTRACT	3.25	data extraction
HKL-2000		data reduction
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: OTDUB

Resolution: 2.2→56.7 Å / Cor.coef. F_o:F_c: 0.951 / Cor.coef. F_o:F_c free: 0.931 / SU B: 7.523 / SU ML: 0.092 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.046 / ESU R Free: 0.037 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2093	5982	4.9 %	RANDOM
R_work	0.1762	-	-	-
obs	0.1778	115715	96.92 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK

Displacement parameters

B_iso max: 165 Å² / B_iso mean: 58.856 Å² / B_iso min: 21.29 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-9.4 Å²	0 Å²	0 Å²
2-	-	-2.83 Å²	0 Å²
3-	-	-	12.23 Å²

Refinement step

Cycle: final / Resolution: 2.2→56.7 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	15348	0	0	476	15824
B_iso mean	-	-	-	51.64	-
Num. residues	-	-	-	-	1948

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.013	0.013	15516
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.017	14878
X-RAY DIFFRACTION	r_angle_refined_deg	1.861	1.64	20944
X-RAY DIFFRACTION	r_angle_other_deg	1.375	1.581	34739
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.655	5	1932
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	41.351	24.9	800
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	20.826	15	3044
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	22.719	15	72
X-RAY DIFFRACTION	r_chiral_restr	0.098	0.2	2141
X-RAY DIFFRACTION	r_gen_planes_refined	0.012	0.02	17028
X-RAY DIFFRACTION	r_gen_planes_other	0.002	0.02	2690

Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-ID	Dom-ID	Auth asym-ID	Number	Rms dev position (Å)
1	1	A	7989	0.11
1	2	E	7989	0.11
2	1	A	8201	0.08
2	2	I	8201	0.08
3	1	A	8019	0.11
3	2	M	8019	0.11
4	1	B	2070	0.14
4	2	C	2070	0.14
5	1	B	2081	0.13
5	2	D	2081	0.13
6	1	B	2239	0.09
6	2	F	2239	0.09
7	1	B	2082	0.13
7	2	G	2082	0.13
8	1	B	2066	0.13
8	2	H	2066	0.13
9	1	B	2258	0.08
9	2	J	2258	0.08
10	1	B	2069	0.13
10	2	K	2069	0.13
11	1	B	2096	0.13
11	2	L	2096	0.13
12	1	B	2227	0.08
12	2	N	2227	0.08
13	1	B	2083	0.13
13	2	O	2083	0.13
14	1	B	2103	0.13
14	2	P	2103	0.13
15	1	C	2191	0.11
15	2	D	2191	0.11
16	1	C	2056	0.14
16	2	F	2056	0.14
17	1	C	2244	0.08
17	2	G	2244	0.08
18	1	C	2164	0.11
18	2	H	2164	0.11
19	1	C	2067	0.14
19	2	J	2067	0.14
20	1	C	2212	0.06
20	2	K	2212	0.06
21	1	C	2208	0.11
21	2	L	2208	0.11
22	1	C	2054	0.14
22	2	N	2054	0.14
23	1	C	2205	0.08
23	2	O	2205	0.08
24	1	C	2206	0.1
24	2	P	2206	0.1
25	1	D	2068	0.13
25	2	F	2068	0.13
26	1	D	2198	0.1
26	2	G	2198	0.1
27	1	D	2212	0.09
27	2	H	2212	0.09
28	1	D	2067	0.14
28	2	J	2067	0.14
29	1	D	2162	0.1
29	2	K	2162	0.1
30	1	D	2257	0.09
30	2	L	2257	0.09
31	1	D	2065	0.13
31	2	N	2065	0.13
32	1	D	2159	0.11
32	2	O	2159	0.11
33	1	D	2229	0.09
33	2	P	2229	0.09
34	1	E	8045	0.1
34	2	I	8045	0.1
35	1	E	8162	0.1
35	2	M	8162	0.1
36	1	F	2061	0.13
36	2	G	2061	0.13
37	1	F	2049	0.13
37	2	H	2049	0.13
38	1	F	2222	0.09
38	2	J	2222	0.09
39	1	F	2050	0.12
39	2	K	2050	0.12
40	1	F	2077	0.13
40	2	L	2077	0.13
41	1	F	2256	0.07
41	2	N	2256	0.07
42	1	F	2067	0.12
42	2	O	2067	0.12
43	1	F	2088	0.13
43	2	P	2088	0.13
44	1	G	2176	0.1
44	2	H	2176	0.1
45	1	G	2068	0.14
45	2	J	2068	0.14
46	1	G	2225	0.05
46	2	K	2225	0.05
47	1	G	2202	0.09
47	2	L	2202	0.09
48	1	G	2059	0.13
48	2	N	2059	0.13
49	1	G	2219	0.07
49	2	O	2219	0.07
50	1	G	2203	0.09
50	2	P	2203	0.09
51	1	H	2067	0.14
51	2	J	2067	0.14
52	1	H	2150	0.1
52	2	K	2150	0.1
53	1	H	2222	0.08
53	2	L	2222	0.08
54	1	H	2064	0.13
54	2	N	2064	0.13
55	1	H	2145	0.11
55	2	O	2145	0.11
56	1	H	2223	0.08
56	2	P	2223	0.08
57	1	I	8076	0.1
57	2	M	8076	0.1
58	1	J	2065	0.13
58	2	K	2065	0.13
59	1	J	2080	0.14
59	2	L	2080	0.14
60	1	J	2227	0.09
60	2	N	2227	0.09
61	1	J	2071	0.13
61	2	O	2071	0.13
62	1	J	2099	0.14
62	2	P	2099	0.14
63	1	K	2172	0.09
63	2	L	2172	0.09
64	1	K	2048	0.12
64	2	N	2048	0.12
65	1	K	2196	0.06
65	2	O	2196	0.06
66	1	K	2182	0.08
66	2	P	2182	0.08
67	1	L	2077	0.13
67	2	N	2077	0.13
68	1	L	2171	0.1
68	2	O	2171	0.1
69	1	L	2242	0.08
69	2	P	2242	0.08
70	1	N	2071	0.13
70	2	O	2071	0.13
71	1	N	2074	0.13
71	2	P	2074	0.13
72	1	O	2169	0.1
72	2	P	2169	0.1

LS refinement shell

Resolution: 2.203→2.261 Å / R_factor R_free error: 0 / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.27	383	-
R_work	0.229	7744	-
all	-	8127	-
obs	-	-	88.36 %

Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

ID	L11 (°²)	L12 (°²)	L13 (°²)	L22 (°²)	L23 (°²)	L33 (°²)	S11 (Å °)	S12 (Å °)	S13 (Å °)	S21 (Å °)	S22 (Å °)	S23 (Å °)	S31 (Å °)	S32 (Å °)	S33 (Å °)	T11 (Å²)	T12 (Å²)	T13 (Å²)	T22 (Å²)	T23 (Å²)	T33 (Å²)	Origin x (Å)	Origin y (Å)	Origin z (Å)
1	0.9564	0.9952	-0.0515	2.0024	-0.086	0.5339	-0.0443	0.0292	-0.0382	-0.1142	-0.0133	-0.0683	0.101	0.1228	0.0576	0.0298	0.033	-0.0086	0.0885	0.0032	0.1158	-37.174	-26.792	27.248
2	0.6954	0.6178	-0.7539	2.867	-1.1086	3.3949	-0.0582	0.0932	0.1718	-0.1816	0.0087	0.0825	-0.2431	-0.0909	0.0495	0.0581	0.0028	-0.054	0.0697	-0.0133	0.158	-47.848	-13.749	18.436
3	1.8381	0.2087	-0.3888	3.0981	-0.6498	3.8839	0.0746	0.2054	0.0767	-0.3089	-0.1674	-0.2335	-0.0227	0.2753	0.0928	0.1271	-0.0213	0.0297	0.2681	-0.0016	0.1877	-8.518	-1.999	13.076
4	1.8777	-0.444	-1.3643	1.7079	0.0353	4.2559	-0.0224	0.3003	-0.0335	-0.3653	0.0109	-0.1287	0.4597	0.0082	0.0115	0.4562	-0.0272	-0.0111	0.2715	0.0083	0.2485	-45.962	-31.867	-5.639
5	1.3201	0.0562	-0.769	0.5072	0.0864	1.1526	0.0332	0.1086	-0.0696	-0.0677	0.0539	0.0337	0.0517	-0.0571	-0.0871	0.0286	-0.0048	-0.0476	0.1197	-0.0052	0.1112	-101.332	-4.489	33.182
6	1.145	0.6841	-1.495	1.5009	-0.6221	3.1792	0.0426	-0.1134	-0.1979	0.1304	-0.0066	-0.0978	0.1974	0.0189	-0.0361	0.0561	-0.0182	-0.0671	0.1229	0.004	0.1639	-93.712	-7.725	50.719
7	1.4207	-1.1441	0.9586	3.3195	-0.9336	0.9989	0.2929	-0.0752	-0.4369	0.0158	-0.1671	0.208	0.5785	-0.2362	-0.1258	0.6126	-0.1942	0.0042	0.3591	-0.0093	0.4855	-126.581	-31.815	46.6
8	1.294	-0.1319	0.0163	4.1845	-0.564	1.2447	-0.0836	0.0389	-0.1321	0.0721	0.0683	-0.0997	0.1693	0.0443	0.0152	0.2295	0.0333	-0.0223	0.188	-0.0232	0.2411	-78.852	-29.718	36.797
9	0.6735	-0.0368	-0.6721	0.4822	-0.0267	1.4026	-0.0046	-0.1086	-0.0195	0.0965	0.0173	-0.064	0.0848	0.1063	-0.0127	0.0363	-0.0047	-0.0332	0.1375	-0.0325	0.1156	-67.127	-10.365	-5.927
10	0.5851	-0.0487	-0.1963	2.6062	1.0734	3.0112	-0.0097	0.0918	-0.0496	-0.252	0.0174	0.0655	0.1411	-0.0341	-0.0077	0.0549	-0.0345	-0.0071	0.1338	-0.0163	0.109	-78.691	-18.232	-18.696
11	2.5963	0.5119	0.3783	3.4319	1.0617	2.0933	0.0123	0.1327	-0.2369	-0.058	0.1212	-0.4245	0.2909	0.2929	-0.1335	0.2441	0.0341	0.0531	0.2159	-0.0092	0.2672	-40.143	-25.439	-32.701
12	2.5238	-0.6254	0.9345	3.3318	-0.3234	2.9762	0.0005	-0.0366	-0.5487	0.2627	0.0321	-0.0982	0.576	0.1447	-0.0326	0.4687	-0.0056	-0.0166	0.2292	0.0021	0.3345	-77.33	-42.498	-0.881
13	1.3974	-0.8258	0.1033	0.7111	-0.0265	0.3078	0.0112	-0.0234	0.0922	-0.0329	-0.0389	-0.0926	-0.0713	0.0824	0.0276	0.0239	-0.0263	-0.0071	0.0673	0.0152	0.1663	-48.019	6.466	40.715
14	1.3212	-0.3195	0.2104	2.5625	-0.5127	2.6444	0.044	-0.0474	-0.0937	-0.0167	0.0028	0.0094	0.0795	-0.1329	-0.0468	0.0088	0.0129	-0.006	0.0688	-0.0031	0.1685	-56.457	-10.758	43.934
15	2.5054	1.2226	-0.506	1.1881	-0.6826	4.0207	0.1362	-0.46	-0.0024	0.438	-0.0836	-0.0207	-0.0304	0.2936	-0.0527	0.309	0.0318	-0.0243	0.3093	-0.0285	0.2585	-24.678	-7.095	69.686
16	2.97	0.5322	-0.3022	3.0208	-0.0101	3.7102	0.057	-0.3668	0.0256	0.4117	-0.1854	-0.0097	-0.0191	0.1172	0.1284	0.0976	-0.0106	-0.0138	0.1995	0.024	0.1356	-72.101	4.435	64.487

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	1 - 259
2	X-RAY DIFFRACTION	1	A	301 - 373
3	X-RAY DIFFRACTION	1	M	320
4	X-RAY DIFFRACTION	2	B	0 - 76
5	X-RAY DIFFRACTION	2	B	101 - 120
6	X-RAY DIFFRACTION	3	C	1 - 76
7	X-RAY DIFFRACTION	3	C	101 - 114
8	X-RAY DIFFRACTION	4	D	1 - 76
9	X-RAY DIFFRACTION	4	D	101 - 105
10	X-RAY DIFFRACTION	5	E	2 - 259
11	X-RAY DIFFRACTION	5	E	301 - 368
12	X-RAY DIFFRACTION	5	F	119
13	X-RAY DIFFRACTION	5	H	113
14	X-RAY DIFFRACTION	5	M	341
15	X-RAY DIFFRACTION	6	F	0 - 76
16	X-RAY DIFFRACTION	7	G	1 - 75
17	X-RAY DIFFRACTION	7	G	101 - 108
18	X-RAY DIFFRACTION	8	H	0 - 75
19	X-RAY DIFFRACTION	9	I	2 - 259
20	X-RAY DIFFRACTION	9	I	301 - 361
21	X-RAY DIFFRACTION	9	J	108
22	X-RAY DIFFRACTION	10	J	0 - 76
23	X-RAY DIFFRACTION	11	K	0 - 74
24	X-RAY DIFFRACTION	11	K	101 - 111
25	X-RAY DIFFRACTION	12	L	1 - 76
26	X-RAY DIFFRACTION	12	L	101 - 107
27	X-RAY DIFFRACTION	13	M	2 - 259
28	X-RAY DIFFRACTION	13	N	104
29	X-RAY DIFFRACTION	13	O	110
30	X-RAY DIFFRACTION	14	N	-1 - 76
31	X-RAY DIFFRACTION	15	O	1 - 75
32	X-RAY DIFFRACTION	15	O	101 - 109
33	X-RAY DIFFRACTION	16	P	0 - 76
34	X-RAY DIFFRACTION	16	P	101 - 116

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