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- PDB-6ups: Crystal structure of the deubiquitylase domain from the Orientia ... -

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Basic information

Entry
Database: PDB / ID: 6ups
TitleCrystal structure of the deubiquitylase domain from the Orientia tsutsugamushi protein OTT_1962 (OtDUB)
ComponentsULP_PROTEASE domain-containing protein
KeywordsHYDROLASE / deubiquitylase / Orientia / CE clan
Function / homologyUbiquitin-like protease family profile. / Ulp1 protease family, C-terminal catalytic domain / Ulp1 protease family, C-terminal catalytic domain / cysteine-type peptidase activity / Papain-like cysteine peptidase superfamily / proteolysis / Ubiquitin-like protease family profile domain-containing protein
Function and homology information
Biological speciesOrientia tsutsugamushi (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å
AuthorsRonau, J.A. / Lim, C.S. / Xiong, Y.
Funding support United States, 3items
OrganizationGrant numberCountry
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
CitationJournal: 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
DepositionOct 18, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 1, 2020Provider: repository / Type: Initial release
Revision 1.1Apr 14, 2021Group: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ULP_PROTEASE domain-containing protein


Theoretical massNumber of molelcules
Total (without water)29,5971
Polymers29,5971
Non-polymers00
Water1,44180
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)114.787, 43.093, 58.244
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein ULP_PROTEASE domain-containing protein


Mass: 29597.367 Da / Num. of mol.: 1 / Fragment: deubiquitylase domain
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, Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 80 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.5 Å3/Da / Density % sol: 50.76 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 0.2 M ammonium iodide, 20% (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-E / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 10, 2017
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 18794 / % possible obs: 91 % / Redundancy: 4.3 % / Rmerge(I) obs: 0.144 / Net I/σ(I): 10.6
Reflection shellResolution: 2→2.07 Å / Redundancy: 4 % / Rmerge(I) obs: 0.825 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 1895 / % possible all: 93.7

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Processing

Software
NameVersionClassification
HKL-2000data reduction
REFMAC5.8.0257refinement
PDB_EXTRACT3.25data extraction
HKL-2000data scaling
SHELXDphasing
RefinementMethod to determine structure: SAD / Resolution: 2→34.67 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.935 / SU B: 11.782 / SU ML: 0.145 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.195 / ESU R Free: 0.165
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2371 919 4.9 %RANDOM
Rwork0.2077 ---
obs0.2092 17880 92.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 105.93 Å2 / Biso mean: 38.339 Å2 / Biso min: 17.35 Å2
Baniso -1Baniso -2Baniso -3
1-3.18 Å20 Å20 Å2
2---0.78 Å20 Å2
3----2.4 Å2
Refinement stepCycle: final / Resolution: 2→34.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1926 0 0 80 2006
Biso mean---42.92 -
Num. residues----245
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0131948
X-RAY DIFFRACTIONr_bond_other_d0.0020.0171833
X-RAY DIFFRACTIONr_angle_refined_deg1.4681.6332639
X-RAY DIFFRACTIONr_angle_other_deg1.5511.5724279
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2215243
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.65825.85999
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.27615348
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.635156
X-RAY DIFFRACTIONr_chiral_restr0.0920.2270
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022144
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02330
LS refinement shellResolution: 2→2.052 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.3 67 -
Rwork0.306 1331 -
all-1398 -
obs--95.17 %
Refinement TLS params.Method: refined / Origin x: 39.76 Å / Origin y: 2.523 Å / Origin z: 28.79 Å
111213212223313233
T0.1062 Å20.0222 Å20.0602 Å2-0.0083 Å20.0187 Å2--0.0775 Å2
L0.49 °20.0837 °20.1132 °2-0.8458 °2-0.0955 °2--1.0022 °2
S-0.0511 Å °-0.0484 Å °-0.0536 Å °-0.0711 Å °-0.0076 Å °-0.0366 Å °0.0085 Å °0.0024 Å °0.0587 Å °

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