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- PDB-3ckd: Crystal structure of the C-terminal domain of the Shigella type I... -

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Basic information

Entry
Database: PDB / ID: 3ckd
TitleCrystal structure of the C-terminal domain of the Shigella type III effector IpaH
ComponentsInvasion plasmid antigen, secreted by the Mxi-Spa secretion machinery
KeywordsLIGASE / E3 ubiquitin ligase / helical / type III effector / Structural Genomics / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homology
Function and homology information


symbiont-mediated suppression of host programmed cell death / effector-mediated activation of programmed cell death in host / : / RING-type E3 ubiquitin transferase / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / ubiquitin-dependent protein catabolic process / host cell cytoplasm / protein ubiquitination / extracellular region
Similarity search - Function
Shigella T3SS effector IpaH domain / Shigella T3SS effector IpaH defines / Novel E3 ligase domain / C-terminal novel E3 ligase, LRR-interacting / LRR-containing bacterial E3 ligase, N-terminal / Type III secretion system leucine rich repeat protein / Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #90 / Leucine-rich repeats, bacterial type / Substrate Binding Domain Of Dnak; Chain:A; Domain 2 / Leucine-rich repeat profile. ...Shigella T3SS effector IpaH domain / Shigella T3SS effector IpaH defines / Novel E3 ligase domain / C-terminal novel E3 ligase, LRR-interacting / LRR-containing bacterial E3 ligase, N-terminal / Type III secretion system leucine rich repeat protein / Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #90 / Leucine-rich repeats, bacterial type / Substrate Binding Domain Of Dnak; Chain:A; Domain 2 / Leucine-rich repeat profile. / Leucine-rich repeat / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Leucine-rich repeat domain superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / E3 ubiquitin-protein ligase ipaH7.8 / RING-type E3 ubiquitin transferase
Similarity search - Component
Biological speciesShigella flexneri 2a str. 301 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.65 Å
AuthorsLam, R. / Singer, A.U. / Cuff, M.E. / Skarina, T. / Kagan, O. / DiLeo, R. / Edwards, A.M. / Joachimiak, A. / Savchenko, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2008
Title: Structure of the Shigella T3SS effector IpaH defines a new class of E3 ubiquitin ligases.
Authors: Singer, A.U. / Rohde, J.R. / Lam, R. / Skarina, T. / Kagan, O. / Dileo, R. / Chirgadze, N.Y. / Cuff, M.E. / Joachimiak, A. / Tyers, M. / Sansonetti, P.J. / Parsot, C. / Savchenko, A.
History
DepositionMar 14, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 25, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Invasion plasmid antigen, secreted by the Mxi-Spa secretion machinery
B: Invasion plasmid antigen, secreted by the Mxi-Spa secretion machinery
C: Invasion plasmid antigen, secreted by the Mxi-Spa secretion machinery
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,4989
Polymers106,9243
Non-polymers5756
Water43224
1
A: Invasion plasmid antigen, secreted by the Mxi-Spa secretion machinery


Theoretical massNumber of molelcules
Total (without water)35,6411
Polymers35,6411
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Invasion plasmid antigen, secreted by the Mxi-Spa secretion machinery
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,7372
Polymers35,6411
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Invasion plasmid antigen, secreted by the Mxi-Spa secretion machinery
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,1206
Polymers35,6411
Non-polymers4785
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)128.928, 128.928, 282.825
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number97
Space group name H-MI422

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Components

#1: Protein Invasion plasmid antigen, secreted by the Mxi-Spa secretion machinery


Mass: 35641.309 Da / Num. of mol.: 3 / Fragment: C-terminal ligase domain: Residues 265-575
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Shigella flexneri 2a str. 301 (bacteria)
Species: Shigella flexneri / Strain: 301 / Serotype 2a / Gene: ipaH1.4, CP0265 / Plasmid: p15-TV-LIC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-Gold(DE3)
References: UniProt: Q8VSA1, UniProt: P18014*PLUS, ubiquitin-protein ligase
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


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


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#5: Water ChemComp-HOH / water / 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 / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.75 Å3/Da / Density % sol: 55.24 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 2M Ammonium sulfate, 1% PEG MME 2000, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97845 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 7, 2006 / Details: Mirrors
RadiationMonochromator: Double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97845 Å / Relative weight: 1
ReflectionResolution: 2.65→50 Å / Num. all: 35079 / Num. obs: 34738 / % possible obs: 99 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 8.2 % / Rmerge(I) obs: 0.073 / Net I/σ(I): 35.3
Reflection shellResolution: 2.65→2.74 Å / Redundancy: 8.1 % / Rmerge(I) obs: 0.479 / Mean I/σ(I) obs: 3.8 / Num. unique all: 3447 / % possible all: 99.5

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
EPICS-basedbeamline controldata collection
dataacquisition systemsdata collection
HKL-2000data reduction
HKL-2000data scaling
SHARPphasing
RefinementMethod to determine structure: SAD / Resolution: 2.65→49.21 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.891 / SU B: 22.903 / SU ML: 0.234 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.561 / ESU R Free: 0.336 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28382 1743 5 %RANDOM
Rwork0.2281 ---
all0.2309 34706 --
obs0.2309 34706 98.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 61.151 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0.01 Å2
Refinement stepCycle: LAST / Resolution: 2.65→49.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6268 0 35 24 6327
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0216402
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5861.9328644
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9515765
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.38324.31355
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.686151099
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.3751557
X-RAY DIFFRACTIONr_chiral_restr0.1170.2948
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024891
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2490.22913
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3140.24355
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1320.2231
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1960.284
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.160.217
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9011.53958
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.52726129
X-RAY DIFFRACTIONr_scbond_it2.63632792
X-RAY DIFFRACTIONr_scangle_it4.1464.52515
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.65→2.719 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.37 112 -
Rwork0.306 2411 -
obs-2523 99.02 %

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