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- PDB-5vbd: Crystal structure of a putative UBL domain of USP9X -

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Basic information

Entry
Database: PDB / ID: 5vbd
TitleCrystal structure of a putative UBL domain of USP9X
ComponentsUSP9X
KeywordsSIGNALING PROTEIN / Ubiquitin / protease / Structural Genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


cytosolic ciliogenesis / K11-linked deubiquitinase activity / positive regulation of TORC2 signaling / protein deubiquitination involved in ubiquitin-dependent protein catabolic process / protein import into peroxisome matrix, receptor recycling / co-SMAD binding / female gamete generation / monoubiquitinated protein deubiquitination / deubiquitinase activity / molecular sequestering activity ...cytosolic ciliogenesis / K11-linked deubiquitinase activity / positive regulation of TORC2 signaling / protein deubiquitination involved in ubiquitin-dependent protein catabolic process / protein import into peroxisome matrix, receptor recycling / co-SMAD binding / female gamete generation / monoubiquitinated protein deubiquitination / deubiquitinase activity / molecular sequestering activity / DNA alkylation repair / protein K63-linked deubiquitination / axon extension / K48-linked deubiquitinase activity / K63-linked deubiquitinase activity / RHOV GTPase cycle / protein deubiquitination / RHOU GTPase cycle / negative regulation of proteasomal ubiquitin-dependent protein catabolic process / cilium assembly / BMP signaling pathway / cysteine-type peptidase activity / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / transforming growth factor beta receptor signaling pathway / chromosome segregation / Peroxisomal protein import / Downregulation of SMAD2/3:SMAD4 transcriptional activity / neuron migration / protein localization / regulation of circadian rhythm / cilium / rhythmic process / cell migration / positive regulation of protein binding / growth cone / ubiquitin-dependent protein catabolic process / ubiquitinyl hydrolase 1 / amyloid fibril formation / cysteine-type deubiquitinase activity / protein stabilization / Ub-specific processing proteases / protein ubiquitination / Amyloid fiber formation / cell division / cysteine-type endopeptidase activity / centrosome / negative regulation of transcription by RNA polymerase II / membrane / nucleus / cytoplasm / cytosol
Similarity search - Function
Probable ubiquitin carboxyl-terminal hydrolase FAF-X / 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. ...Probable ubiquitin carboxyl-terminal hydrolase FAF-X / 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
Ubiquitinyl hydrolase 1 / Ubiquitin carboxyl-terminal hydrolase 9X
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.5 Å
AuthorsDong, A. / Chern, Y. / Hou, F. / Li, Y. / Tempel, W. / Bountra, C. / Arrowsmith, C.H. / Edwards, A.M. / Tong, Y. / Structural Genomics Consortium (SGC)
CitationJournal: to be published
Title: Crystal structure of a putative UBL domain of USP9X
Authors: Chern, Y. / Dong, A. / Hou, F. / Li, Y. / Tempel, W. / Bountra, C. / Arrowsmith, C.H. / Edwards, A.M. / Tong, Y. / Structural Genomics Consortium (SGC)
History
DepositionMar 29, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 26, 2017Provider: repository / Type: Initial release
Revision 1.1Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: USP9X


Theoretical massNumber of molelcules
Total (without water)12,4424
Polymers12,4421
Non-polymers03
Water1,13563
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: USP9X

A: USP9X


Theoretical massNumber of molelcules
Total (without water)24,8848
Polymers24,8842
Non-polymers06
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area4600 Å2
ΔGint-32 kcal/mol
Surface area11350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.723, 125.294, 29.546
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-1001-

UNX

21A-1002-

UNX

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Components

#1: Protein USP9X


Mass: 12442.154 Da / Num. of mol.: 1 / Fragment: putative UBL domain (UNP residues 705-795)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: USP9X, hCG_18381 / Plasmid: pET28-MHL / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: D3DWB6, UniProt: Q93008*PLUS
#2: Chemical ChemComp-UNX / UNKNOWN ATOM OR ION


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


Mass: 18.015 Da / Num. of mol.: 63 / 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: 1.74 Å3/Da / Density % sol: 29.22 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 20% PEG 8000, 0.2 M NaCl, 0.1 M HEPES pH7.5, 5% MPD

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97914 Å
DetectorType: DECTRIS PILATUS3 X 6M / Detector: PIXEL / Date: Nov 28, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97914 Å / Relative weight: 1
ReflectionResolution: 1.5→50 Å / Num. obs: 14247 / % possible obs: 99.8 % / Redundancy: 11.7 % / Rmerge(I) obs: 0.058 / Rpim(I) all: 0.018 / Rrim(I) all: 0.061 / Χ2: 1.171 / Net I/σ(I): 7.5 / Num. measured all: 166545
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.5-1.5310.10.8570.8910.2780.9020.5299.9
1.53-1.5510.70.7480.9090.2360.7860.564100
1.55-1.5811.10.6620.9250.2050.6930.576100
1.58-1.6210.40.5890.9210.190.620.609100
1.62-1.6512.10.4810.9450.1440.5020.667100
1.65-1.6912.60.3830.9630.1130.3990.747100
1.69-1.7312.30.3270.9630.0970.3410.81899.9
1.73-1.7812.30.2470.9860.0740.2580.953100
1.78-1.83120.220.9840.0660.230.989100
1.83-1.8911.60.1730.990.0530.1811.143100
1.89-1.9611.20.1430.9910.0450.151.276100
1.96-2.0412.70.1190.9950.0350.1251.36399.9
2.04-2.1312.30.0990.9950.030.1031.484100
2.13-2.2412.20.0860.9960.0260.0891.462100
2.24-2.38120.0760.9980.0230.0791.47399.7
2.38-2.5611.50.0680.9980.0210.0721.566100
2.56-2.8212.70.0640.9970.0190.0671.60599.9
2.82-3.2312.10.0580.9980.0170.0611.7899.7
3.23-4.0711.10.0490.9980.0150.0511.84598.9
4.07-5010.90.0460.9960.0150.0481.63199.2

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
REFMAC5.8.0158refinement
PDB_EXTRACT3.22data extraction
Arcimboldophasing
Coot0.8.8model building
HKL-3000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.5→50 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.959 / SU B: 2.024 / SU ML: 0.075 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.095 / ESU R Free: 0.087
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY. The choice of the asymmetric unit is ambiguous due to the break in the main chain, crystal symmetry ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY. The choice of the asymmetric unit is ambiguous due to the break in the main chain, crystal symmetry provides alternatives for bridging of the gap between residues 894 to 900.
RfactorNum. reflection% reflectionSelection details
Rfree0.236 713 5 %RANDOM
Rwork0.2271 ---
obs0.2276 13525 98.85 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 65.81 Å2 / Biso mean: 31.182 Å2 / Biso min: 19.48 Å2
Baniso -1Baniso -2Baniso -3
1-2.06 Å20 Å2-0 Å2
2---0.89 Å20 Å2
3----1.16 Å2
Refinement stepCycle: final / Resolution: 1.5→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms653 0 3 64 720
Biso mean--30 40.72 -
Num. residues----85
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.019733
X-RAY DIFFRACTIONr_bond_other_d0.0020.02685
X-RAY DIFFRACTIONr_angle_refined_deg1.4261.9371000
X-RAY DIFFRACTIONr_angle_other_deg0.91531587
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.914598
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.06624.33330
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.16815130
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.907157
X-RAY DIFFRACTIONr_chiral_restr0.0860.2116
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02835
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02149
LS refinement shellResolution: 1.499→1.538 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.322 43 -
Rwork0.318 867 -
all-910 -
obs--86.75 %

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