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- PDB-7w3r: USP34 catalytic domain -

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Basic information

Entry
Database: PDB / ID: 7w3r
TitleUSP34 catalytic domain
ComponentsUbiquitin carboxyl-terminal hydrolase 34
KeywordsHYDROLASE / USP34 in isolation
Function / homology
Function and homology information


protein K48-linked deubiquitination / protein deubiquitination / TCF dependent signaling in response to WNT / Wnt signaling pathway / positive regulation of canonical Wnt signaling pathway / ubiquitin-dependent protein catabolic process / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / Ub-specific processing proteases / cysteine-type endopeptidase activity ...protein K48-linked deubiquitination / protein deubiquitination / TCF dependent signaling in response to WNT / Wnt signaling pathway / positive regulation of canonical Wnt signaling pathway / ubiquitin-dependent protein catabolic process / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / Ub-specific processing proteases / cysteine-type endopeptidase activity / nucleus / cytosol
Similarity search - Function
Domain of unknown function DUF3517 / Domain of unknown function (DUF3517) / Ubiquitin specific protease (USP) domain signature 2. / Ubiquitin specific protease (USP) domain signature 1. / Ubiquitin specific protease, conserved site / Peptidase C19, ubiquitin carboxyl-terminal hydrolase / Ubiquitin carboxyl-terminal hydrolase / Ubiquitin specific protease domain / Ubiquitin specific protease (USP) domain profile. / Papain-like cysteine peptidase superfamily / Armadillo-type fold
Similarity search - Domain/homology
Ubiquitin carboxyl-terminal hydrolase 34
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.92 Å
AuthorsXu, G.L. / Ming, Z.H.
Funding support2items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31700052
National Natural Science Foundation of China (NSFC)81871938
CitationJournal: J.Mol.Biol. / Year: 2022
Title: Structural Insights into the Catalytic Mechanism and Ubiquitin Recognition of USP34.
Authors: Xu, G. / Su, H. / Lu, L. / Liu, X. / Zhao, L. / Tang, B. / Ming, Z.
History
DepositionNov 26, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 1, 2022Provider: repository / Type: Initial release
Revision 1.1Jun 15, 2022Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.title
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ubiquitin carboxyl-terminal hydrolase 34
B: Ubiquitin carboxyl-terminal hydrolase 34
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,8613
Polymers89,7962
Non-polymers651
Water3,963220
1
A: Ubiquitin carboxyl-terminal hydrolase 34
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,9632
Polymers44,8981
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Ubiquitin carboxyl-terminal hydrolase 34


Theoretical massNumber of molelcules
Total (without water)44,8981
Polymers44,8981
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)50.120, 128.060, 64.400
Angle α, β, γ (deg.)90.000, 93.490, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Ubiquitin carboxyl-terminal hydrolase 34 / Deubiquitinating enzyme 34 / Ubiquitin thioesterase 34 / Ubiquitin-specific-processing protease 34


Mass: 44897.805 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: USP34, KIAA0570, KIAA0729
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q70CQ2, ubiquitinyl hydrolase 1
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 220 / 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: 2.3 Å3/Da / Density % sol: 46.46 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop
Details: 16% w/v PEG 3350, 0.16M sodium bromide, 0.125M Magnesium formate dihydrate, 0.025M BIS-TRIS

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.979183 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Jan 12, 2020
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979183 Å / Relative weight: 1
ReflectionResolution: 1.92→32.47 Å / Num. obs: 60503 / % possible obs: 98.1 % / Redundancy: 14.83 % / Rmerge(I) obs: 0.048 / Net I/σ(I): 19.3
Reflection shellResolution: 1.92→1.989 Å / Num. unique obs: 60396 / CC1/2: 0.998

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Processing

Software
NameVersionClassification
PHENIX1.15_3459refinement
PDB_EXTRACT3.27data extraction
xia2data reduction
xia2data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5wch

5wch


Resolution: 1.92→25.014 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 32.25 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2615 2990 4.95 %
Rwork0.2259 57406 -
obs0.2277 60396 97.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 106.32 Å2 / Biso mean: 50.2922 Å2 / Biso min: 24.41 Å2
Refinement stepCycle: final / Resolution: 1.92→25.014 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5462 0 1 220 5683
Biso mean--41.37 50.77 -
Num. residues----666
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.92-1.95150.40651390.3832268996
1.9515-1.98510.32551290.2922274898
1.9851-2.02120.28611420.2748270397
2.0212-2.06010.32771410.2716273999
2.0601-2.10210.37281380.2859269397
2.1021-2.14780.26721680.2504274899
2.1478-2.19770.26431350.2616270398
2.1977-2.25260.41621270.3807259593
2.2526-2.31350.3541610.3165261395
2.3135-2.38150.27641490.2557275498
2.3815-2.45830.31911720.2507273399
2.4583-2.54610.29631500.2519271398
2.5461-2.6480.33451350.2474277199
2.648-2.76830.33211460.25273899
2.7683-2.91410.33121520.2555276799
2.9141-3.09630.261090.2445277699
3.0963-3.33490.263960.237282598
3.3349-3.66960.27191550.2179271798
3.6696-4.19840.2151610.1906278699
4.1984-5.28130.19431390.1673279499
5.2813-25.0140.2211460.2061280199
Refinement TLS params.Method: refined / Origin x: 39.6403 Å / Origin y: 66.3117 Å / Origin z: 60.5029 Å
111213212223313233
T0.2901 Å2-0.0133 Å20.0638 Å2-0.2667 Å20.0579 Å2--0.2514 Å2
L1.4349 °20.4763 °21.0405 °2-0.6869 °20.5158 °2--0.8805 °2
S-0.0731 Å °0.0484 Å °0.041 Å °0.0416 Å °0.0444 Å °0.076 Å °-0.1628 Å °0.0366 Å °0.0368 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA1892 - 2261
2X-RAY DIFFRACTION1allA2289
3X-RAY DIFFRACTION1allB1891 - 2266
4X-RAY DIFFRACTION1allS1 - 220

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