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- PDB-4mem: Crystal Structure of the rat USP11 DUSP-UBL domains -

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Basic information

Entry
Database: PDB / ID: 4mem
TitleCrystal Structure of the rat USP11 DUSP-UBL domains
ComponentsUbiquitin carboxyl-terminal hydrolase 11
KeywordsHYDROLASE / DOMAIN PRESENT IN UBIQUITIN SPECIFIC PROTEASES (DUSP) / UBIQUITIN-LIKE DOMAIN (UBL) / DU FINGER / UBIQUITIN THIOLESTERASE / DEUBIQUITINATING ENZYME (DUB)
Function / homology
Function and homology information


Ub-specific processing proteases / protein deubiquitination / transcription corepressor binding / chromosome / ubiquitin-dependent protein catabolic process / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / cysteine-type endopeptidase activity / nucleus / cytoplasm
Similarity search - Function
DUSP-like / DUSP-like / Ubiquitin-like domain, USP-type / Ubiquitin-like domain / Peptidase C19, ubiquitin-specific peptidase, DUSP domain / DUSP-like superfamily / DUSP domain / DUSP domain profile. / Domain in ubiquitin-specific proteases. / : ...DUSP-like / DUSP-like / Ubiquitin-like domain, USP-type / Ubiquitin-like domain / Peptidase C19, ubiquitin-specific peptidase, DUSP domain / DUSP-like superfamily / DUSP domain / DUSP domain profile. / Domain in ubiquitin-specific proteases. / : / 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. / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Papain-like cysteine peptidase superfamily / Ubiquitin-like (UB roll) / Roll / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Ubiquitin carboxyl-terminal hydrolase 11
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.34 Å
AuthorsHarper, S. / Gratton, H.E. / Cornaciu, I. / Oberer, M. / Scott, D.J. / Emsley, J. / Dreveny, I.
CitationJournal: Biochemistry / Year: 2014
Title: Structure and Catalytic Regulatory Function of Ubiquitin Specific Protease 11 N-Terminal and Ubiquitin-like Domains.
Authors: Harper, S. / Gratton, H.E. / Cornaciu, I. / Oberer, M. / Scott, D.J. / Emsley, J. / Dreveny, I.
History
DepositionAug 27, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 7, 2014Provider: repository / Type: Initial release
Revision 1.1May 28, 2014Group: Database references
Revision 1.2Sep 20, 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ubiquitin carboxyl-terminal hydrolase 11
B: Ubiquitin carboxyl-terminal hydrolase 11


Theoretical massNumber of molelcules
Total (without water)52,9312
Polymers52,9312
Non-polymers00
Water95553
1
A: Ubiquitin carboxyl-terminal hydrolase 11


Theoretical massNumber of molelcules
Total (without water)26,4661
Polymers26,4661
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Ubiquitin carboxyl-terminal hydrolase 11


Theoretical massNumber of molelcules
Total (without water)26,4661
Polymers26,4661
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: Ubiquitin carboxyl-terminal hydrolase 11

B: Ubiquitin carboxyl-terminal hydrolase 11


Theoretical massNumber of molelcules
Total (without water)52,9312
Polymers52,9312
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_655x+1,y,z1
Buried area1990 Å2
ΔGint-16 kcal/mol
Surface area23080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.285, 80.156, 149.269
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121
Detailsbiological assembly is a monomer. There are 2 biological units in the asymmetric unit (chain A chain B).

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Components

#1: Protein Ubiquitin carboxyl-terminal hydrolase 11


Mass: 26465.500 Da / Num. of mol.: 2 / Fragment: DUSP-UBL domains, UNP residues 19-237
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Strain: 10116 / Gene: rCG_42884, Usp11 / Plasmid: pET26b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q5D006, ubiquitinyl hydrolase 1
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 53 / 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: 1

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Sample preparation

CrystalDensity Matthews: 2.11 Å3/Da / Density % sol: 41.62 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 6.77
Details: 0.15 M Malic Acid, 24% w/v PEG 3350, 10 mM Strontium Chloride, pH 6.77, VAPOR DIFFUSION, SITTING DROP, temperature 292K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.973 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Jun 22, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.973 Å / Relative weight: 1
ReflectionResolution: 2.292→74.635 Å / Num. obs: 20914 / % possible obs: 99.7 % / Redundancy: 11.4 %

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Processing

Software
NameVersionClassificationNB
SCALAdata scaling
PHENIX1.8.2_1309refinement
PDB_EXTRACT3.11data extraction
MxCuBEdata collection
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4MEL

4mel


Resolution: 2.34→54.622 Å / Occupancy max: 1 / Occupancy min: 0.5 / SU ML: 0.31 / Isotropic thermal model: isotropic / σ(F): 1.34 / Phase error: 28 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2643 996 5.07 %
Rwork0.2206 --
obs0.2228 19660 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 54.9952 Å2
Refinement stepCycle: LAST / Resolution: 2.34→54.622 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3495 0 0 53 3548
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0043613
X-RAY DIFFRACTIONf_angle_d0.9164925
X-RAY DIFFRACTIONf_dihedral_angle_d13.5361335
X-RAY DIFFRACTIONf_chiral_restr0.036524
X-RAY DIFFRACTIONf_plane_restr0.005642
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3401-2.46340.3421110.29992622X-RAY DIFFRACTION100
2.4634-2.61780.32531400.29312611X-RAY DIFFRACTION100
2.6178-2.81990.35631390.27862621X-RAY DIFFRACTION100
2.8199-3.10360.30861570.2492639X-RAY DIFFRACTION100
3.1036-3.55270.25871580.22532625X-RAY DIFFRACTION100
3.5527-4.47570.19031490.17182691X-RAY DIFFRACTION100
4.4757-54.63720.25581420.19722855X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.43241.5738-1.42492.8283-0.88261.2332-0.05910.0102-0.10380.03080.04960.04110.0053-0.12030.02740.31380.0309-0.01120.3705-0.00590.3412-16.065217.137187.8067
22.1241-1.1325-0.13653.0437-2.01571.7432-0.09420.0645-0.0097-0.04260.15890.23990.1569-0.2107-0.03420.4476-0.0463-0.05730.4516-0.00240.43-17.865-15.0875100.5098
33.0963-0.3017-0.1153.43421.61093.9034-0.00150.1143-0.0345-0.1091-0.00620.1764-0.0112-0.0935-0.0050.31860.0352-0.00930.3260.00080.3212-41.37217.6158138.7792
43.6301-0.15150.43223.05880.82783.4027-0.2052-0.1220.16450.12090.2547-0.08460.09040.0902-0.02840.4610.079-0.00730.4976-0.00450.3621-40.5015-19.6132112.5875
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A and resid 26:146
2X-RAY DIFFRACTION2chain A and resid 147:237
3X-RAY DIFFRACTION3chain B and resid 27:144
4X-RAY DIFFRACTION4chain B and resid 145:242

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