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- PDB-4wz2: Crystal structure of U-box 2 of LubX / LegU2 / Lpp2887 from Legio... -

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Basic information

Entry
Database: PDB / ID: 4wz2
TitleCrystal structure of U-box 2 of LubX / LegU2 / Lpp2887 from Legionella pneumophila str. Paris, Ile175Met mutant
ComponentsE3 ubiquitin-protein ligase LubX
KeywordsLIGASE / alpha/beta protein / effector / structural genomics / PSI-Biology / Midwest Center for Structural Genomics / MCSG
Function / homology
Function and homology information


cellular response to misfolded protein / protein quality control for misfolded or incompletely synthesized proteins / positive regulation of proteolysis / RING-type E3 ubiquitin transferase / protein polyubiquitination / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / host cell / protein-folding chaperone binding / proteasome-mediated ubiquitin-dependent protein catabolic process ...cellular response to misfolded protein / protein quality control for misfolded or incompletely synthesized proteins / positive regulation of proteolysis / RING-type E3 ubiquitin transferase / protein polyubiquitination / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / host cell / protein-folding chaperone binding / proteasome-mediated ubiquitin-dependent protein catabolic process / protein ubiquitination / extracellular region / cytoplasm
Similarity search - Function
U-box domain / U-box domain profile. / Modified RING finger domain / U-box domain / Zinc/RING finger domain, C3HC4 (zinc finger) / Herpes Virus-1 / Zinc finger, RING/FYVE/PHD-type / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
HEXANE-1,6-DIOL / E3 ubiquitin-protein ligase LubX
Similarity search - Component
Biological speciesLegionella pneumophila (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.408 Å
AuthorsStogios, P.J. / Qualie, A.T. / Skarina, T. / Nocek, B. / Di Leo, R. / Yim, V. / Savchenko, A. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM094585 United States
Department of Energy (DOE, United States)DE-AC02-06CH11357 United States
CitationJournal: Structure / Year: 2015
Title: Molecular Characterization of LubX: Functional Divergence of the U-Box Fold by Legionella pneumophila.
Authors: Quaile, A.T. / Urbanus, M.L. / Stogios, P.J. / Nocek, B. / Skarina, T. / Ensminger, A.W. / Savchenko, A.
History
DepositionNov 18, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 28, 2015Provider: repository / Type: Initial release
Revision 1.1Jul 29, 2015Group: Database references
Revision 1.2Aug 19, 2015Group: Database references
Revision 1.3Sep 20, 2017Group: Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: E3 ubiquitin-protein ligase LubX
B: E3 ubiquitin-protein ligase LubX
C: E3 ubiquitin-protein ligase LubX
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,0629
Polymers35,5183
Non-polymers5446
Water43224
1
A: E3 ubiquitin-protein ligase LubX
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,9933
Polymers11,8391
Non-polymers1542
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: E3 ubiquitin-protein ligase LubX
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,1944
Polymers11,8391
Non-polymers3553
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: E3 ubiquitin-protein ligase LubX
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,8752
Polymers11,8391
Non-polymers351
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)160.033, 160.033, 160.033
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number207
Space group name H-MP432
Components on special symmetry positions
IDModelComponents
11C-301-

CL

21C-402-

HOH

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Components

#1: Protein E3 ubiquitin-protein ligase LubX / Legionella U-box protein


Mass: 11839.427 Da / Num. of mol.: 3 / Mutation: I175M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Legionella pneumophila (bacteria) / Strain: Paris / Gene: lubX, lpp2887 / Plasmid: p15TV-LIC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q5X159, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases)
#2: Chemical
ChemComp-HEZ / HEXANE-1,6-DIOL


Mass: 118.174 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H14O2
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 24 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 4.81 Å3/Da / Density % sol: 74.42 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 15 mg/ml protein, 1.6 M ammonium sulfate, 0.1 M HEPES (pH 7.5) and 2% hexanediol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9790433 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 7, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9790433 Å / Relative weight: 1
ReflectionResolution: 3.4→40 Å / Num. obs: 9956 / % possible obs: 98.6 % / Redundancy: 6.5 % / Rmerge(I) obs: 0.126 / Net I/σ(I): 14.21
Reflection shellResolution: 3.4→3.46 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.649 / Mean I/σ(I) obs: 2.97 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-3000data reduction
PHENIXphasing
PHENIXmodel building
Cootmodel building
PHENIX(phenix.refine: 1.9_1692)refinement
HKL-3000data scaling
RefinementMethod to determine structure: SAD / Resolution: 3.408→37.72 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 18.7 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflectionSelection details
Rfree0.2156 948 10.08 %Random selection
Rwork0.1775 ---
obs0.1813 9409 93.17 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.408→37.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1812 0 34 24 1870
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051870
X-RAY DIFFRACTIONf_angle_d0.5352511
X-RAY DIFFRACTIONf_dihedral_angle_d12.758721
X-RAY DIFFRACTIONf_chiral_restr0.025290
X-RAY DIFFRACTIONf_plane_restr0.003313
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.408-3.58760.29331160.24351012X-RAY DIFFRACTION81
3.5876-3.81220.25121290.20131138X-RAY DIFFRACTION90
3.8122-4.10620.24351340.17991174X-RAY DIFFRACTION93
4.1062-4.51880.19591370.15231239X-RAY DIFFRACTION98
4.5188-5.17120.16571400.15251267X-RAY DIFFRACTION97
5.1712-6.50980.20881430.18761272X-RAY DIFFRACTION97
6.5098-37.72240.20481490.16921359X-RAY DIFFRACTION95

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