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- PDB-4xzx: Shigella flexneri effector OspI C62S mutant -

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Basic information

Entry
Database: PDB / ID: 4xzx
TitleShigella flexneri effector OspI C62S mutant
ComponentsORF169b
KeywordsIMMUNE SYSTEM / shigella / flexneri / effector / deamidase
Function / homologyCathepsin B; Chain A - #140 / : / : / Shigella glutamine deamidase OspI / Cathepsin B; Chain A / Alpha-Beta Complex / Alpha Beta / ACETATE ION / ORF169b
Function and homology information
Biological speciesShigella flexneri (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsNishide, A. / Takagi, K. / Minsoo, K. / Sasakawa, C. / Mizushima, T.
CitationJournal: To Be Published
Title: New insights into the active site structure of Shigella effecter OspI
Authors: Nishide, A. / Takagi, K. / Minsoo, K. / Sasakawa, C. / Mizushima, T.
History
DepositionFeb 5, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 10, 2016Provider: repository / Type: Initial release
Revision 1.1Feb 5, 2020Group: Data collection / Derived calculations / Category: diffrn_source / pdbx_struct_oper_list
Item: _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation
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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ORF169b
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,1942
Polymers24,1351
Non-polymers591
Water2,000111
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area210 Å2
ΔGint1 kcal/mol
Surface area9740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.368, 91.962, 68.101
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein ORF169b / Ospi


Mass: 24134.807 Da / Num. of mol.: 1 / Mutation: C62S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Shigella flexneri (bacteria) / Gene: ORF169b / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q8VSD5
#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 111 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.29 Å3/Da / Density % sol: 46.34 %
Crystal growTemperature: 288 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.2M magnesium acetate, 0.1M sodium cacodylate, 20% PEG8000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: BRUKER SMART 6500 / Detector: CCD / Date: Jul 26, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 11184 / % possible obs: 99.9 % / Redundancy: 7.2 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 14.3
Reflection shellResolution: 2.2→2.24 Å / Redundancy: 7.4 % / Rmerge(I) obs: 0.245 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3B21

3b21


Resolution: 2.2→38.11 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.901 / SU B: 5.234 / SU ML: 0.134 / Cross valid method: THROUGHOUT / ESU R: 0.248 / ESU R Free: 0.215 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24581 552 5 %RANDOM
Rwork0.1774 ---
obs0.18079 10572 99.32 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 13.092 Å2
Baniso -1Baniso -2Baniso -3
1--0.15 Å2-0 Å2-0 Å2
2--0.17 Å2-0 Å2
3----0.01 Å2
Refinement stepCycle: 1 / Resolution: 2.2→38.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1491 0 4 111 1606
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0191523
X-RAY DIFFRACTIONr_bond_other_d0.0010.021405
X-RAY DIFFRACTIONr_angle_refined_deg1.7171.9422053
X-RAY DIFFRACTIONr_angle_other_deg0.87533250
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7255191
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.33825.67674
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.17315267
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.79155
X-RAY DIFFRACTIONr_chiral_restr0.1040.2221
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021758
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02345
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_it1.0561.159768
X-RAY DIFFRACTIONr_mcbond_other1.0561.158766
X-RAY DIFFRACTIONr_mcangle_it1.7581.73957
X-RAY DIFFRACTIONr_mcangle_other1.7571.732958
X-RAY DIFFRACTIONr_scbond_it1.971.385755
X-RAY DIFFRACTIONr_scbond_other1.9691.385756
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.2971.9861097
X-RAY DIFFRACTIONr_long_range_B_refined4.4589.5271840
X-RAY DIFFRACTIONr_long_range_B_other4.4579.5271841
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.201→2.258 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.335 38 -
Rwork0.236 738 -
obs--97.12 %

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