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- PDB-2g43: Structure of the ZNF UBP domain from deubiquitinating enzyme isop... -

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Basic information

Entry
Database: PDB / ID: 2g43
TitleStructure of the ZNF UBP domain from deubiquitinating enzyme isopeptidase T (IsoT)
ComponentsUbiquitin carboxyl-terminal hydrolase 5
KeywordsHYDROLASE / Zinc Finger / deubiquitinating enzyme
Function / homology
Function and homology information


protein K48-linked deubiquitination / deubiquitinase activity / negative regulation of ubiquitin-dependent protein catabolic process / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / ubiquitin binding / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / lysosome / Ub-specific processing proteases ...protein K48-linked deubiquitination / deubiquitinase activity / negative regulation of ubiquitin-dependent protein catabolic process / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / ubiquitin binding / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / lysosome / Ub-specific processing proteases / protein ubiquitination / cysteine-type endopeptidase activity / proteolysis / zinc ion binding / nucleus / cytosol
Similarity search - Function
Ubiquitin carboxyl-terminal hydrolase 5, UBA1 domain / Ubiquitinyl hydrolase / Ubiquitinyl hydrolase, variant UBP zinc finger / Variant UBP zinc finger / : / Ubiquitin Carboxyl-terminal Hydrolase-like zinc finger / Zinc finger, UBP-type / Zn-finger in ubiquitin-hydrolases and other protein / Zinc finger UBP-type profile. / UBA/TS-N domain ...Ubiquitin carboxyl-terminal hydrolase 5, UBA1 domain / Ubiquitinyl hydrolase / Ubiquitinyl hydrolase, variant UBP zinc finger / Variant UBP zinc finger / : / Ubiquitin Carboxyl-terminal Hydrolase-like zinc finger / Zinc finger, UBP-type / Zn-finger in ubiquitin-hydrolases and other protein / Zinc finger UBP-type profile. / UBA/TS-N domain / Ubiquitin specific protease (USP) domain signature 2. / Ubiquitin specific protease (USP) domain signature 1. / Ubiquitin specific protease, conserved site / Ubiquitin associated domain / Peptidase C19, ubiquitin carboxyl-terminal hydrolase / Ubiquitin carboxyl-terminal hydrolase / Ubiquitin specific protease domain / Ubiquitin specific protease (USP) domain profile. / Ubiquitin-associated domain / Ubiquitin-associated domain (UBA) profile. / UBA-like superfamily / Zinc/RING finger domain, C3HC4 (zinc finger) / Herpes Virus-1 / Papain-like cysteine peptidase superfamily / Zinc finger, RING/FYVE/PHD-type / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Ubiquitin carboxyl-terminal hydrolase 5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.09 Å
AuthorsReyes-Turcu, F.E. / Horton, J.R. / Mullally, J.E. / Heroux, A. / Cheng, X. / Wilkinson, K.D.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2006
Title: The Ubiquitin Binding Domain ZnF UBP Recognizes the C-Terminal Diglycine Motif of Unanchored Ubiquitin.
Authors: Reyes-Turcu, F.E. / Horton, J.R. / Mullally, J.E. / Heroux, A. / Cheng, X. / Wilkinson, K.D.
History
DepositionFeb 21, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 4, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Remark 600HETEROGEN THREE UNKOWN ATOMS, UNX 61, 65 AND 66 FORM A TRIANGULAR STRUCTURE.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ubiquitin carboxyl-terminal hydrolase 5
B: Ubiquitin carboxyl-terminal hydrolase 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,3187
Polymers29,1872
Non-polymers1315
Water1,27971
1
A: Ubiquitin carboxyl-terminal hydrolase 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,6592
Polymers14,5931
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Ubiquitin carboxyl-terminal hydrolase 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,6595
Polymers14,5931
Non-polymers654
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)61.380, 86.180, 59.900
Angle α, β, γ (deg.)90.00, 99.29, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Ubiquitin carboxyl-terminal hydrolase 5 / Ubiquitin thiolesterase 5 / Ubiquitin-specific processing protease 5 / Deubiquitinating enzyme 5 / ...Ubiquitin thiolesterase 5 / Ubiquitin-specific processing protease 5 / Deubiquitinating enzyme 5 / Isopeptidase T


Mass: 14593.387 Da / Num. of mol.: 2
Fragment: The Zn Finger UMP domain of IsoT (residues 163-291)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: USP5, ISOT / Production host: Escherichia coli (E. coli) / References: UniProt: P45974, EC: 3.1.2.15
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 3 / Source method: obtained synthetically
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 71 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 2.68 Å3/Da / Density % sol: 54.06 %
Crystal growTemperature: 300 K / pH: 6.5
Details: 16% polyethylene glycol 8000, 0.8 M sodium cacodylate pH 6.5, 0.16 M calcium acetate, 20% glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 300K, pH 6.50

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X26C / Wavelength: 1.28020, 1.2790, 1.12810 0.97623
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: May 5, 2005
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1NSLS X26CMADMx-ray1
2Mx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
11.28021
21.2791
31.12811
40.976231
ReflectionResolution: 2.09→35 Å / Num. obs: 17788 / % possible obs: 96.7 % / Observed criterion σ(I): -3 / Redundancy: 2.8 % / Biso Wilson estimate: 21.2 Å2 / Rmerge(I) obs: 0.047 / Net I/σ(I): 27.7
Reflection shellResolution: 2.09→2.16 Å / Rmerge(I) obs: 0.064 / Mean I/σ(I) obs: 16.7 / % possible all: 97.2

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Processing

Software
NameVersionClassification
HKL-2000data collection
SCALEPACKdata scaling
SOLVEphasing
CNS1.1refinement
HKL-2000data reduction
RefinementMethod to determine structure: MAD / Resolution: 2.09→35 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 445910.92 / Data cutoff low absF: 0 / Isotropic thermal model: OVERALL ANISOTROPIC B VALUE / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.274 1743 5 %RANDOM
Rwork0.228 ---
obs0.228 17788 96.7 %-
all-17788 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 46.06 Å2 / ksol: 0.39 e/Å3
Displacement parametersBiso mean: 41.5 Å2
Baniso -1Baniso -2Baniso -3
1--7.05 Å20 Å21.41 Å2
2--3.72 Å20 Å2
3---3.33 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.33 Å0.3 Å
Luzzati d res low-35 Å
Luzzati sigma a0.2 Å0.21 Å
Refinement stepCycle: LAST / Resolution: 2.09→35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1757 0 5 71 1833
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d24.2
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.82
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.581.5
X-RAY DIFFRACTIONc_mcangle_it2.642
X-RAY DIFFRACTIONc_scbond_it2.452
X-RAY DIFFRACTIONc_scangle_it3.792.5
LS refinement shellResolution: 2.09→2.16 Å / Rfactor Rfree error: 0.025 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.3 146 4.5 %
Rwork0.289 3097 -
obs--89.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2dna-rna_rep.param
X-RAY DIFFRACTION4water_rep.param
X-RAY DIFFRACTION5ion.param

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