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- PDB-3w30: Structual basis for the recognition of Ubc13 by the Shigella flex... -

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Basic information

Entry
Database: PDB / ID: 3w30
TitleStructual basis for the recognition of Ubc13 by the Shigella flexneri effector OspI
ComponentsORF169b
KeywordsIMMUNE SYSTEM / Type 3 secretion system / Effector / Deamidation
Function / homologyCathepsin B; Chain A - #140 / : / : / Shigella glutamine deamidase OspI / symbiont-mediated suppression of host TRAF-mediated signal transduction / Cathepsin B; Chain A / Alpha-Beta Complex / Alpha Beta / ORF169b
Function and homology information
Biological speciesShigella flexneri (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.99 Å
AuthorsNishide, A. / Kim, M. / Takagi, K. / Sasakawa, C. / Mizushima, T.
CitationJournal: J.Mol.Biol. / Year: 2013
Title: Structural Basis for the Recognition of Ubc13 by the Shigella flexneri Effector OspI.
Authors: Nishide, A. / Kim, M. / Takagi, K. / Himeno, A. / Sanada, T. / Sasakawa, C. / Mizushima, T.
History
DepositionDec 7, 2012Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 27, 2013Provider: repository / Type: Initial release
Revision 1.1Jul 17, 2013Group: Database references
Revision 1.2Nov 8, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ORF169b
B: ORF169b


Theoretical massNumber of molelcules
Total (without water)48,2382
Polymers48,2382
Non-polymers00
Water00
1
A: ORF169b


Theoretical massNumber of molelcules
Total (without water)24,1191
Polymers24,1191
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: ORF169b


Theoretical massNumber of molelcules
Total (without water)24,1191
Polymers24,1191
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)67.583, 67.352, 84.840
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein ORF169b


Mass: 24118.807 Da / Num. of mol.: 2 / Mutation: C62A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Shigella flexneri (bacteria) / Gene: ORF169b, CP0209 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8VSD5

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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: 2.01 Å3/Da / Density % sol: 38.91 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.2M Magnesium Acetate, 0.1M Tris-HCl (pH6.5), 25% (w/v) PEG 8000, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorDate: Jan 1, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.99→50 Å / Num. obs: 8233 / % possible obs: 100 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.141

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3B21

3b21


Resolution: 2.99→30 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.876 / SU B: 20.272 / SU ML: 0.387 / Cross valid method: THROUGHOUT / ESU R Free: 0.572 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.30283 375 4.6 %RANDOM
Rwork0.22953 ---
obs0.23285 7773 98.79 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 10.794 Å2
Baniso -1Baniso -2Baniso -3
1--0.04 Å20 Å20 Å2
2---0.06 Å20 Å2
3---0.1 Å2
Refinement stepCycle: LAST / Resolution: 2.99→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2980 0 0 0 2980
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0213038
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5771.944098
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2265382
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.34325.676148
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.64415532
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.2431510
X-RAY DIFFRACTIONr_chiral_restr0.0930.2442
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0212318
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5521.51902
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.08423054
X-RAY DIFFRACTIONr_scbond_it1.61531136
X-RAY DIFFRACTIONr_scangle_it2.7384.51044
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.989→3.066 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.385 26 -
Rwork0.253 510 -
obs--88.6 %

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