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- PDB-4xi1: Crystal structure of U-box 2 of LubX / LegU2 / Lpp2887 from Legio... -

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Basic information

Entry
Database: PDB / ID: 4xi1
TitleCrystal structure of U-box 2 of LubX / LegU2 / Lpp2887 from Legionella pneumophila str. Paris, wild-type
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 / Z disc / protein polyubiquitination / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / host cell / protein-folding chaperone binding ...cellular response to misfolded protein / protein quality control for misfolded or incompletely synthesized proteins / positive regulation of proteolysis / RING-type E3 ubiquitin transferase / Z disc / 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
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 / MOLECULAR REPLACEMENT / Resolution: 2.983 Å
AuthorsStogios, P.J. / Quaile, T. / Skarina, T. / Cuff, M. / Di Leo, R. / Yim, V. / Savchenko, A. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
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
DepositionJan 6, 2015Deposition site: RCSB / Processing site: RCSB
SupersessionJan 21, 2015ID: 4WZ1
Revision 1.0Jan 21, 2015Provider: repository / Type: Initial release
Revision 1.1Jul 29, 2015Group: Other
Revision 1.2Aug 26, 2015Group: Database references
Revision 1.3Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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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)36,07711
Polymers35,3233
Non-polymers7548
Water1,56787
1
A: E3 ubiquitin-protein ligase LubX
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,9283
Polymers11,7741
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)12,1034
Polymers11,7741
Non-polymers3283
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: E3 ubiquitin-protein ligase LubX
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,0464
Polymers11,7741
Non-polymers2723
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
A: E3 ubiquitin-protein ligase LubX
B: E3 ubiquitin-protein ligase LubX
C: E3 ubiquitin-protein ligase LubX
hetero molecules

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)72,15522
Polymers70,6476
Non-polymers1,50816
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation13_556y,x,-z+11
Buried area13600 Å2
ΔGint-8 kcal/mol
Surface area21930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)160.227, 160.227, 160.227
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-302-

CL

21C-303-

HEZ

31C-411-

HOH

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Components

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


Mass: 11774.493 Da / Num. of mol.: 3 / Fragment: UNP residues 102-202
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Legionella pneumophila (strain Paris) (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-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Chemical
ChemComp-HEZ / HEXANE-1,6-DIOL


Mass: 118.174 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C6H14O2
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 87 / 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: 4.85 Å3/Da / Density % sol: 74.65 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 15 mg/ml protein, V8 protease (1:100), 1.6 M ammonium sulfate, 0.1 M HEPES pH 7.5 and 2% hexanediol

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
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: 2.98→20 Å / Num. obs: 13171 / % possible obs: 88.7 % / Redundancy: 5.7 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 23.58
Reflection shellResolution: 2.98→3.03 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.623 / Mean I/σ(I) obs: 2.7 / % possible all: 92.7

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.9_1692)refinement
HKL-3000data reduction
PHENIXmodel building
PHENIXphasing
Cootmodel building
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4WZ2

4wz2


Resolution: 2.983→19.874 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 22.42 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2095 659 5 %Random selection
Rwork0.1623 ---
obs0.1647 13167 88.65 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.983→19.874 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1836 0 48 87 1971
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091908
X-RAY DIFFRACTIONf_angle_d1.0522561
X-RAY DIFFRACTIONf_dihedral_angle_d16.849733
X-RAY DIFFRACTIONf_chiral_restr0.043295
X-RAY DIFFRACTIONf_plane_restr0.004317
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9825-3.21190.30781330.24682532X-RAY DIFFRACTION92
3.2119-3.53350.26381330.19372527X-RAY DIFFRACTION92
3.5335-4.04110.23151330.15962508X-RAY DIFFRACTION90
4.0411-5.07730.15231310.13292485X-RAY DIFFRACTION88
5.0773-19.87410.19941290.15472456X-RAY DIFFRACTION82
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)
15.8613-1.06090.25278.6093-1.68994.59510.01590.03250.7563-0.7020.0265-0.2233-1.0008-0.0496-0.04230.9792-0.02490.04880.47160.09030.559735.728247.425664.9005
22.81532.25341.19593.9045-2.49076.5944-0.41620.6640.3352-1.02340.73140.2128-0.0816-1.5431-0.28121.34790.0844-0.12650.8980.09850.749227.067946.176356.5317
33.6452-1.66233.18829.02281.8894.217-0.3782-0.69160.77170.0435-0.4522-0.2714-1.1455-0.17180.74530.6835-0.12280.05050.6740.04550.611338.564646.525578.5951
43.6428-1.4956-2.80646.9602-1.15339.40560.33280.5758-0.0169-0.7806-0.193-0.3478-0.21450.7504-0.03760.5814-0.08430.08430.55210.03090.460644.624731.835362.317
54.41721.3772-5.12753.51031.13398.37610.6776-0.15420.64960.02960.1547-0.679-1.09341.7657-0.7910.8199-0.24280.11821.2196-0.00570.867955.6236.188165.1997
65.21954.3687-1.38284.3514-2.91826.11660.35670.4891-1.16760.0287-0.1208-1.07530.2889-0.0551-0.14810.70380.0179-0.00810.4867-0.02250.508832.879924.786667.4456
73.8535-0.84620.0095.9203-2.43086.89730.32490.0175-0.1703-0.2942-0.31580.42080.1214-0.1728-0.00230.4066-0.0584-0.1160.51670.01430.606513.347125.411877.1715
88.98921.17740.04971.9504-1.21024.7324-0.0026-0.9756-0.23160.0679-0.1010.18470.1760.22640.08560.5030.0308-0.01830.5311-0.00350.5467.072927.0987.5404
98.25261.6677-6.79876.4952-1.00885.65380.2090.85530.5302-0.2460.25150.248-0.8498-0.4996-0.36230.4599-0.0561-0.12070.61010.09130.675323.191631.295969.6408
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A and resi 123:158
2X-RAY DIFFRACTION2chain A and resi 159:182
3X-RAY DIFFRACTION3chain A and resi 183:198
4X-RAY DIFFRACTION4chain B and resi 124:158
5X-RAY DIFFRACTION5chain B and resi 159:182
6X-RAY DIFFRACTION6chain B and resi 183:198
7X-RAY DIFFRACTION7chain C and resi 123:158
8X-RAY DIFFRACTION8chain C and resi 159:182
9X-RAY DIFFRACTION9chain C and resi 183:197

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