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- PDB-5kyb: Crystal structure of the apo-form of USP7 catalytic domain [V302K... -

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Basic information

Entry
Database: PDB / ID: 5kyb
TitleCrystal structure of the apo-form of USP7 catalytic domain [V302K] mutant
ComponentsUbiquitin carboxyl-terminal hydrolase 7
KeywordsHYDROLASE / USP7 catalytic domain / deubiquitinase / V302K mutant
Function / homology
Function and homology information


regulation of telomere capping / regulation of establishment of protein localization to telomere / monoubiquitinated protein deubiquitination / regulation of retrograde transport, endosome to Golgi / deubiquitinase activity / DNA alkylation repair / regulation of DNA-binding transcription factor activity / K48-linked deubiquitinase activity / symbiont-mediated disruption of host cell PML body / negative regulation of NF-kappaB transcription factor activity ...regulation of telomere capping / regulation of establishment of protein localization to telomere / monoubiquitinated protein deubiquitination / regulation of retrograde transport, endosome to Golgi / deubiquitinase activity / DNA alkylation repair / regulation of DNA-binding transcription factor activity / K48-linked deubiquitinase activity / symbiont-mediated disruption of host cell PML body / negative regulation of NF-kappaB transcription factor activity / negative regulation of gene expression via chromosomal CpG island methylation / protein deubiquitination / negative regulation of gluconeogenesis / negative regulation of TORC1 signaling / transcription-coupled nucleotide-excision repair / negative regulation of proteasomal ubiquitin-dependent protein catabolic process / Regulation of PTEN localization / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / regulation of signal transduction by p53 class mediator / regulation of circadian rhythm / PML body / regulation of protein stability / Transcription-Coupled Nucleotide Excision Repair (TC-NER) / Formation of TC-NER Pre-Incision Complex / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / p53 binding / rhythmic process / Regulation of TP53 Degradation / chromosome / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / Ub-specific processing proteases / protein stabilization / protein ubiquitination / nuclear body / cysteine-type endopeptidase activity / protein-containing complex / proteolysis / nucleoplasm / nucleus / cytosol
Similarity search - Function
ubp-family deubiquitinating enzyme superfamily / ubp-family deubiquitinating enzyme fold / Ubiquitin carboxyl-terminal hydrolase 7, ICP0-binding domain / ICP0-binding domain of Ubiquitin-specific protease 7 / Ubiquitin carboxyl-terminal hydrolase, C-terminal / Ubiquitin-specific protease C-terminal / MATH domain / : / MATH/TRAF domain / MATH/TRAF domain profile. ...ubp-family deubiquitinating enzyme superfamily / ubp-family deubiquitinating enzyme fold / Ubiquitin carboxyl-terminal hydrolase 7, ICP0-binding domain / ICP0-binding domain of Ubiquitin-specific protease 7 / Ubiquitin carboxyl-terminal hydrolase, C-terminal / Ubiquitin-specific protease C-terminal / MATH domain / : / MATH/TRAF domain / MATH/TRAF domain profile. / meprin and TRAF homology / TRAF-like / 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. / Single Sheet / Papain-like cysteine peptidase superfamily / Mainly Beta
Similarity search - Domain/homology
Ubiquitin carboxyl-terminal hydrolase 7
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.2 Å
AuthorsRouge, L. / Ozen, A.
CitationJournal: Structure / Year: 2018
Title: Selectively Modulating Conformational States of USP7 Catalytic Domain for Activation.
Authors: Ozen, A. / Rouge, L. / Bashore, C. / Hearn, B.R. / Skelton, N.J. / Dueber, E.C.
History
DepositionJul 21, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 9, 2017Provider: repository / Type: Initial release
Revision 1.1Feb 20, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _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
Revision 1.2Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ubiquitin carboxyl-terminal hydrolase 7
B: Ubiquitin carboxyl-terminal hydrolase 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,4204
Polymers81,2362
Non-polymers1842
Water3,099172
1
A: Ubiquitin carboxyl-terminal hydrolase 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,7102
Polymers40,6181
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Ubiquitin carboxyl-terminal hydrolase 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,7102
Polymers40,6181
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)75.620, 68.280, 77.060
Angle α, β, γ (deg.)90.000, 95.990, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Ubiquitin carboxyl-terminal hydrolase 7 / Deubiquitinating enzyme 7 / Herpesvirus-associated ubiquitin-specific protease / Ubiquitin ...Deubiquitinating enzyme 7 / Herpesvirus-associated ubiquitin-specific protease / Ubiquitin thioesterase 7 / Ubiquitin-specific-processing protease 7


Mass: 40617.930 Da / Num. of mol.: 2 / Fragment: UNP residues 1-76 / Mutation: V302K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: USP7, HAUSP / Production host: Escherichia coli (E. coli) / References: UniProt: Q93009, ubiquitinyl hydrolase 1
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 172 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.44 Å3/Da / Density % sol: 49.5 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 1% Tryptone, 0.05M HEPES Na pH 7.0, 20% PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 9, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.2→56.72 Å / Num. obs: 39712 / % possible obs: 99.6 % / Redundancy: 3.3 % / Biso Wilson estimate: 41.67 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.054 / Rpim(I) all: 0.035 / Rrim(I) all: 0.065 / Net I/σ(I): 10 / Num. measured all: 131027 / Scaling rejects: 3
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Diffraction-ID% possible all
2.2-2.273.30.5410.805199.3
9.07-56.723.50.0270.999199.7

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
MOSFLM7.1.1data reduction
Aimless0.2.8data scaling
PHASER1.10.1phasing
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.2data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1NB8

1nb8


Resolution: 2.2→56.719 Å / SU ML: 0.32 / Cross valid method: NONE / σ(F): 1.33 / Phase error: 34.54
RfactorNum. reflection% reflection
Rfree0.2763 2000 5.06 %
Rwork0.2128 --
obs0.216 39552 99.22 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 211.54 Å2 / Biso mean: 54.4187 Å2 / Biso min: 29.19 Å2
Refinement stepCycle: final / Resolution: 2.2→56.719 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5381 0 12 172 5565
Biso mean--55.53 48.91 -
Num. residues----662
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0145504
X-RAY DIFFRACTIONf_angle_d1.1987412
X-RAY DIFFRACTIONf_chiral_restr0.064790
X-RAY DIFFRACTIONf_plane_restr0.007963
X-RAY DIFFRACTIONf_dihedral_angle_d15.7573324
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.2001-2.25510.34451370.31172664280199
2.2551-2.31610.34821470.28492661280899
2.3161-2.38420.37651380.28262648278699
2.3842-2.46120.35431420.262654279699
2.4612-2.54920.3251410.25672686282799
2.5492-2.65120.38041430.24782671281499
2.6512-2.77190.30451400.23782674281499
2.7719-2.9180.33841510.24232677282899
2.918-3.10080.32371400.239726832823100
3.1008-3.34020.31811420.229526842826100
3.3402-3.67630.25771450.21462697284299
3.6763-4.20810.24971450.18822694283999
4.2081-5.30120.23251410.160727122853100
5.3012-56.73790.21291480.19092747289598

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