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- PDB-9i77: Deubiquitinase DUB16 from Leishmania donovani -

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Basic information

Entry
Database: PDB / ID: 9i77
TitleDeubiquitinase DUB16 from Leishmania donovani
ComponentsUbiquitin carboxyl-terminal hydrolase
KeywordsLIGASE / Ubiquitin / Leishmania / Protease
Function / homology
Function and homology information


protein deubiquitination / ubiquitin-dependent protein catabolic process / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / cytoplasm
Similarity search - Function
Peptidase C12, ubiquitin carboxyl-terminal hydrolase superfamily / Ubiquitin carboxyl-terminal hydrolase, family 1 / Ubiquitin carboxyl-terminal hydrolase (UCH) catalytic domain profile. / Peptidase C12, ubiquitin carboxyl-terminal hydrolase / Papain-like cysteine peptidase superfamily
Similarity search - Domain/homology
Ubiquitin carboxyl-terminal hydrolase
Similarity search - Component
Biological speciesLeishmania donovani (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsBrannigan, J.A. / Dodson, E.J. / Wilkinson, A.J.
Funding support United Kingdom, 3items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom)MR/P027989/1 United Kingdom
Wellcome Trust200807/Z/16/Z United Kingdom
Wellcome Trust223045/Z/21/Z United Kingdom
CitationJournal: Biochem.J. / Year: 2025
Title: Structure and activity of the essential UCH family deubiquitinase DUB16 from Leishmania donovani.
Authors: Brannigan, J.A. / Kamran, M. / Jones, N.G. / Nightingale, E.M. / Dodson, E.J. / Ejazi, S.A. / Mottram, J.C. / Ali, N. / Wilkinson, A.J.
History
DepositionJan 31, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 9, 2025Provider: repository / Type: Initial release
Revision 1.1Jul 16, 2025Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.2Sep 17, 2025Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ubiquitin carboxyl-terminal hydrolase
B: Ubiquitin carboxyl-terminal hydrolase


Theoretical massNumber of molelcules
Total (without water)50,8052
Polymers50,8052
Non-polymers00
Water3,837213
1
A: Ubiquitin carboxyl-terminal hydrolase


Theoretical massNumber of molelcules
Total (without water)25,4031
Polymers25,4031
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Ubiquitin carboxyl-terminal hydrolase


Theoretical massNumber of molelcules
Total (without water)25,4031
Polymers25,4031
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)86.4, 86.4, 125.57
Angle α, β, γ (deg.)90, 90, 120
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-338-

HOH

21A-392-

HOH

31B-376-

HOH

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Components

#1: Protein Ubiquitin carboxyl-terminal hydrolase


Mass: 25402.717 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: DUB16 with a vestigial GPA at the N-terminus arising from HRV 3C cleavage of the affinity purification tag
Source: (gene. exp.) Leishmania donovani (eukaryote) / Gene: CGC20_27140, CGC21_8200, LDBPK_250190, LDHU3_25.0250 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: A0A504WVB8, ubiquitinyl hydrolase 1
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 213 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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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: 2.66 Å3/Da / Density % sol: 53.81 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: Sitting drops composed of equal volumes of protein at 16 mg.ml-1 in 150 mM NaCl, 25 mM Tris-HCl pH 8.0, 1 mM DTT and a crystallisation solution of 1.9 M ammonium sulphate in bis-Tris propane buffer (pH 7.0)
PH range: 7.0 - 8.0 / Temp details: Room temperature

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9762 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Dec 1, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 1.69→74.48 Å / Num. obs: 60298 / % possible obs: 100 % / Redundancy: 19.7 % / CC1/2: 1 / Rmerge(I) obs: 0.06 / Rpim(I) all: 0.019 / Rrim(I) all: 0.063 / Χ2: 0.59 / Net I/σ(I): 19.4
Reflection shell

% possible all: 99.8

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2
9.11-74.48170.02290.146510.0070.0240.67
1.69-1.7218.33.7380.530840.421.293.9560.32

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Processing

Software
NameVersionClassification
DIALSdata collection
autoPROCdata processing
xia2data reduction
MOLREPphasing
BUCCANEERmodel building
REFMAC5.8.0430 (refmacat 0.4.88)refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→74.48 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.961 / SU B: 4.202 / SU ML: 0.121 / Cross valid method: FREE R-VALUE / ESU R: 0.106 / ESU R Free: 0.106
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2425 3018 5.009 %
Rwork0.2106 57232 -
all0.212 --
obs-60250 99.98 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 44.257 Å2
Baniso -1Baniso -2Baniso -3
1--0.56 Å2-0.28 Å20 Å2
2---0.56 Å20 Å2
3---1.817 Å2
Refinement stepCycle: LAST / Resolution: 1.7→74.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3395 0 0 213 3608
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0123506
X-RAY DIFFRACTIONr_bond_other_d0.0010.0163319
X-RAY DIFFRACTIONr_angle_refined_deg1.6031.84776
X-RAY DIFFRACTIONr_angle_other_deg0.5611.7437635
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8315451
X-RAY DIFFRACTIONr_dihedral_angle_2_deg13.421519
X-RAY DIFFRACTIONr_dihedral_angle_3_deg1410552
X-RAY DIFFRACTIONr_dihedral_angle_6_deg14.37210155
X-RAY DIFFRACTIONr_chiral_restr0.0790.2551
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.024176
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02768
X-RAY DIFFRACTIONr_nbd_refined0.2260.2721
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1930.22926
X-RAY DIFFRACTIONr_nbtor_refined0.1770.21748
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0810.21844
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1990.2209
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0250.23
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1640.217
X-RAY DIFFRACTIONr_nbd_other0.1460.2130
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2090.217
X-RAY DIFFRACTIONr_mcbond_it3.8874.1441810
X-RAY DIFFRACTIONr_mcbond_other3.8864.1441810
X-RAY DIFFRACTIONr_mcangle_it5.1947.4142259
X-RAY DIFFRACTIONr_mcangle_other5.1967.4152260
X-RAY DIFFRACTIONr_scbond_it4.6344.6421696
X-RAY DIFFRACTIONr_scbond_other4.6324.6431697
X-RAY DIFFRACTIONr_scangle_it6.9948.292517
X-RAY DIFFRACTIONr_scangle_other6.9938.292518
X-RAY DIFFRACTIONr_lrange_it8.80741.0433897
X-RAY DIFFRACTIONr_lrange_other8.73240.6283849
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.7440.42270.44168X-RAY DIFFRACTION99.773
1.744-1.7920.3762200.3764066X-RAY DIFFRACTION100
1.792-1.8440.3642220.3643977X-RAY DIFFRACTION100
1.844-1.90.3291830.3293842X-RAY DIFFRACTION100
1.9-1.9620.3362010.3083752X-RAY DIFFRACTION100
1.962-2.0310.3092350.2823575X-RAY DIFFRACTION100
2.031-2.1080.2671490.253543X-RAY DIFFRACTION100
2.108-2.1940.291570.2423377X-RAY DIFFRACTION100
2.194-2.2910.3091750.2283220X-RAY DIFFRACTION100
2.291-2.4030.2971990.2343081X-RAY DIFFRACTION99.9695
2.403-2.5330.2841520.2272971X-RAY DIFFRACTION100
2.533-2.6860.3011440.2152793X-RAY DIFFRACTION100
2.686-2.8720.2751380.2062652X-RAY DIFFRACTION100
2.872-3.1010.2531100.212478X-RAY DIFFRACTION100
3.101-3.3970.2681050.2212279X-RAY DIFFRACTION100
3.397-3.7970.2331370.2032038X-RAY DIFFRACTION100
3.797-4.3820.2051000.1621834X-RAY DIFFRACTION100
4.382-5.3630.131730.1311587X-RAY DIFFRACTION100
5.363-7.5640.202610.1931251X-RAY DIFFRACTION100
7.564-100.134300.134749X-RAY DIFFRACTION99.8718

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