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

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Basic information

Entry
Database: PDB / ID: 3naw
TitleCrystal structure of E. coli O157:H7 effector protein NleL
Componentssecreted effector protein
KeywordsLIGASE / 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
E3 ubiquitin-protein ligase SopA / E3 ubiquitin-protein ligase SopA
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.5 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)140,64920
Polymers138,8562
Non-polymers1,79318
Water5,314295
1
A: secreted effector protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,1819
Polymers69,4281
Non-polymers7538
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: secreted effector protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,46811
Polymers69,4281
Non-polymers1,04010
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7730 Å2
ΔGint-106 kcal/mol
Surface area51120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)313.672, 77.310, 61.508
Angle α, β, γ (deg.)90.00, 94.54, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein secreted effector protein


Mass: 69427.969 Da / Num. of mol.: 2 / Fragment: UNP residues 176-782
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: O157:H7 / Gene: ECs1560 / Plasmid: pMCSG20 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) RIL / References: UniProt: Q8X5G6, UniProt: A0A0H3JDV8*PLUS
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 295 / 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: 2.69 Å3/Da / Density % sol: 54.23 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 0.1M MES, 1.6M LiSO4 or MgSO4, 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: 1.0115, 0.9794, 0.9796, 0.9494
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 28, 2009 / Details: Mirrors
RadiationMonochromator: GRAPHITE / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.01151
20.97941
30.97961
40.94941
ReflectionResolution: 2.5→50 Å / Num. all: 51029 / Num. obs: 50366 / % possible obs: 98.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.6 % / Rsym value: 0.118 / Net I/σ(I): 12.6
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 7 % / Mean I/σ(I) obs: 3.8 / Rsym value: 0.581 / % possible all: 97.4

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Processing

Software
NameVersionClassification
Blu-Icedata collection
SOLVEphasing
PHENIX(phenix.refine: 1.5_2)refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MAD / Resolution: 2.5→47.047 Å / SU ML: 0.38 / Isotropic thermal model: Anisotropic / σ(F): 0.2 / Phase error: 27.27 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2465 2528 5.13 %
Rwork0.1839 --
obs0.1872 49261 96.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 45.981 Å2 / ksol: 0.325 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-15.1259 Å20 Å2-7.919 Å2
2---6.0185 Å20 Å2
3----9.1075 Å2
Refinement stepCycle: LAST / Resolution: 2.5→47.047 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9640 0 106 295 10041
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0099940
X-RAY DIFFRACTIONf_angle_d1.07813446
X-RAY DIFFRACTIONf_dihedral_angle_d19.5673550
X-RAY DIFFRACTIONf_chiral_restr0.0751449
X-RAY DIFFRACTIONf_plane_restr0.0041736
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.54810.34511260.22722349X-RAY DIFFRACTION87
2.5481-2.60010.30571280.21672521X-RAY DIFFRACTION93
2.6001-2.65660.2891290.20962457X-RAY DIFFRACTION94
2.6566-2.71840.29491350.21042511X-RAY DIFFRACTION94
2.7184-2.78640.28121440.21372572X-RAY DIFFRACTION95
2.7864-2.86170.27781360.20062561X-RAY DIFFRACTION96
2.8617-2.94590.26311480.20232575X-RAY DIFFRACTION96
2.9459-3.0410.32611410.20522577X-RAY DIFFRACTION97
3.041-3.14970.29121470.21512583X-RAY DIFFRACTION97
3.1497-3.27570.26321520.20362626X-RAY DIFFRACTION98
3.2757-3.42480.25721470.19082650X-RAY DIFFRACTION98
3.4248-3.60530.27311340.17822639X-RAY DIFFRACTION98
3.6053-3.83110.20541360.15832679X-RAY DIFFRACTION98
3.8311-4.12670.21311400.14462645X-RAY DIFFRACTION99
4.1267-4.54170.1941500.13292669X-RAY DIFFRACTION99
4.5417-5.19810.2011470.14382678X-RAY DIFFRACTION99
5.1981-6.54630.24441300.18292696X-RAY DIFFRACTION99
6.5463-47.0550.19941580.17962745X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 114.8966 Å / Origin y: 32.3124 Å / Origin z: 30.7755 Å
111213212223313233
T0.1142 Å20.039 Å2-0.0249 Å2-0.1445 Å20.0049 Å2--0.1402 Å2
L0.282 °2-0.0203 °20.0478 °2-0.5172 °20.1407 °2--0.6732 °2
S-0.1124 Å °-0.0296 Å °0.0578 Å °-0.0443 Å °-0.0131 Å °0.097 Å °-0.0458 Å °-0.1479 Å °0.116 Å °
Refinement TLS groupSelection details: all

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