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- PDB-3nb2: Crystal structure of E. coli O157:H7 effector protein NleL -

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Basic information

Entry
Database: PDB / ID: 3nb2
TitleCrystal structure of E. coli O157:H7 effector protein NleL
Componentssecreted effector protein
KeywordsLIGASE / secreted effector protein / pentapeptide / HECT domain / HECT E3 ubiquitin ligase
Function / homology
Function and homology information


HECT-type E3 ubiquitin transferase / ubiquitin-protein transferase activity / protein ubiquitination / extracellular region
Similarity search - Function
effector protein (NleL) fold / effector protein (NleL) / Putative secreted effector protein / HECT-like ubiquitin ligase fold / HECT-like ubiquitin ligase / E3 ubiquitin ligase SopA-like central domain / SopA-like central domain / E3 ubiquitin-protein ligase SopA-like, catalytic domain / SopA-like, catalytic domain superfamily / SopA-like catalytic domain ...effector protein (NleL) fold / effector protein (NleL) / Putative secreted effector protein / HECT-like ubiquitin ligase fold / HECT-like ubiquitin ligase / E3 ubiquitin ligase SopA-like central domain / SopA-like central domain / E3 ubiquitin-protein ligase SopA-like, catalytic domain / SopA-like, catalytic domain superfamily / SopA-like catalytic domain / Pentapeptide repeats (8 copies) / E3 ubiquitin-protein ligase SopA / Pentapeptide repeat / Pectate Lyase C-like / 3 Solenoid / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
2,3-DIHYDROXY-1,4-DITHIOBUTANE / E3 ubiquitin-protein ligase SopA / E3 ubiquitin-protein ligase SopA
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsLin, D.Y. / Chen, J.
CitationJournal: J.Biol.Chem. / Year: 2011
Title: Biochemical and Structural Studies of a HECT-like Ubiquitin Ligase from Escherichia coli O157:H7.
Authors: Lin, D.Y. / Diao, J. / Zhou, D. / Chen, J.
History
DepositionJun 2, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 27, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 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 / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: secreted effector protein
B: secreted effector protein
C: secreted effector protein
D: secreted effector protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)283,20456
Polymers277,7124
Non-polymers5,49252
Water19,7801098
1
A: secreted effector protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,35920
Polymers69,4281
Non-polymers1,93119
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: secreted effector protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,0858
Polymers69,4281
Non-polymers6577
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: secreted effector protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,09816
Polymers69,4281
Non-polymers1,67015
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: secreted effector protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,66312
Polymers69,4281
Non-polymers1,23511
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)177.013, 124.203, 154.900
Angle α, β, γ (deg.)90.00, 107.60, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
secreted effector protein


Mass: 69427.969 Da / Num. of mol.: 4 / Fragment: UNP residues 171-782
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: O157:H7 / Gene: ECs1560, GI:13361024 / Plasmid: pMCSG20 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) RIL / References: UniProt: Q8X5G6, UniProt: A0A0H3JDV8*PLUS

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Non-polymers , 5 types, 1150 molecules

#2: Chemical...
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 29 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical
ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-DTT / 2,3-DIHYDROXY-1,4-DITHIOBUTANE / 1,4-DITHIOTHREITOL


Mass: 154.251 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O2S2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1098 / 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: 2.93 Å3/Da / Density % sol: 57.96 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 0.1M Mes, 1.6M LiSO4, 16% Glyerol, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.07223 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 28, 2008 / Details: Mirrors
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.07223 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. all: 186206 / Num. obs: 185647 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Rsym value: 0.06 / Net I/σ(I): 22.1
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 3.8 % / Mean I/σ(I) obs: 2.6 / Rsym value: 0.547 / % possible all: 100

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Processing

Software
NameVersionClassification
Blu-Icedata collection
PHASERphasing
PHENIX(phenix.refine: 1.5_2)refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3NAW

3naw


Resolution: 2.1→44.738 Å / SU ML: 0.31 / Isotropic thermal model: Anisotropic / σ(F): 1.89 / Phase error: 24.38 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2314 9326 5.03 %
Rwork0.1836 --
obs0.186 185585 99.45 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 43.199 Å2 / ksol: 0.344 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.4398 Å2-0 Å21.0757 Å2
2--1.9649 Å20 Å2
3----1.5251 Å2
Refinement stepCycle: LAST / Resolution: 2.1→44.738 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19382 0 330 1098 20810
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00820105
X-RAY DIFFRACTIONf_angle_d1.0227176
X-RAY DIFFRACTIONf_dihedral_angle_d18.8847221
X-RAY DIFFRACTIONf_chiral_restr0.0732922
X-RAY DIFFRACTIONf_plane_restr0.0043501
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.1210.33492770.26835540X-RAY DIFFRACTION93
2.121-2.14590.29993180.24535831X-RAY DIFFRACTION100
2.1459-2.17210.30773050.23235873X-RAY DIFFRACTION100
2.1721-2.19960.28083260.22725871X-RAY DIFFRACTION100
2.1996-2.22850.28743040.23245877X-RAY DIFFRACTION100
2.2285-2.2590.30783200.22875905X-RAY DIFFRACTION100
2.259-2.29130.29333280.21265845X-RAY DIFFRACTION100
2.2913-2.32550.24873060.20795867X-RAY DIFFRACTION100
2.3255-2.36190.28283230.21285889X-RAY DIFFRACTION100
2.3619-2.40060.26713140.20565962X-RAY DIFFRACTION100
2.4006-2.4420.27353070.19935833X-RAY DIFFRACTION100
2.442-2.48640.30533150.21045862X-RAY DIFFRACTION100
2.4864-2.53420.26623030.20815916X-RAY DIFFRACTION100
2.5342-2.58590.26372860.20355950X-RAY DIFFRACTION100
2.5859-2.64210.28093120.21265888X-RAY DIFFRACTION100
2.6421-2.70360.27252920.20885909X-RAY DIFFRACTION100
2.7036-2.77120.28443410.21885868X-RAY DIFFRACTION100
2.7712-2.84610.28453280.2145887X-RAY DIFFRACTION100
2.8461-2.92980.24633080.20725873X-RAY DIFFRACTION100
2.9298-3.02440.24663240.19985888X-RAY DIFFRACTION100
3.0244-3.13240.2433450.1975850X-RAY DIFFRACTION100
3.1324-3.25780.25963190.19895919X-RAY DIFFRACTION100
3.2578-3.4060.21142940.18525916X-RAY DIFFRACTION100
3.406-3.58550.21632980.17045913X-RAY DIFFRACTION100
3.5855-3.81010.19113040.15855914X-RAY DIFFRACTION100
3.8101-4.10410.18152780.14685929X-RAY DIFFRACTION100
4.1041-4.51670.16523260.12745907X-RAY DIFFRACTION100
4.5167-5.16950.15953100.13415922X-RAY DIFFRACTION99
5.1695-6.50980.20652980.16725884X-RAY DIFFRACTION99
6.5098-44.74780.21713170.17315771X-RAY DIFFRACTION95
Refinement TLS params.Method: refined / Origin x: -42.3929 Å / Origin y: 33.0393 Å / Origin z: 36.0663 Å
111213212223313233
T0.1817 Å2-0.0463 Å20.0031 Å2-0.1286 Å2-0.0054 Å2--0.1336 Å2
L0.5173 °2-0.038 °2-0.0297 °2-0.0615 °20.0087 °2--0.038 °2
S0.0044 Å °-0.0889 Å °-0.0198 Å °0.0053 Å °-0.0021 Å °0.0139 Å °0.0168 Å °0.0077 Å °-0.004 Å °
Refinement TLS groupSelection details: all

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