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- PDB-3gz2: Crystal structure of IpgC in complex with an IpaB peptide -

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Basic information

Entry
Database: PDB / ID: 3gz2
TitleCrystal structure of IpgC in complex with an IpaB peptide
Components
  • Chaperone protein ipgC
  • Invasin ipaB
KeywordsCHAPERONE / Tetratricopeptide repeat / TPR / chaperone binding region / Virulence / Secreted / Transmembrane
Function / homology
Function and homology information


host cell membrane / host cell nucleus / extracellular region / membrane / identical protein binding / cytoplasm
Similarity search - Function
Type III secretion system, invasin protein B / Invasin IpaB, N-terminal / Type III cell invasion protein SipB / Secretion system effector C, SseC-like / Secretion system effector C (SseC) like family / Tetratricopeptide TPR-3 / Tetratricopeptide repeat / Type III secretion system, low calcium response, chaperone LcrH/SycD, subgroup / Type III secretion system, low calcium response, chaperone LcrH/SycD / Tetratricopeptide repeat domain ...Type III secretion system, invasin protein B / Invasin IpaB, N-terminal / Type III cell invasion protein SipB / Secretion system effector C, SseC-like / Secretion system effector C (SseC) like family / Tetratricopeptide TPR-3 / Tetratricopeptide repeat / Type III secretion system, low calcium response, chaperone LcrH/SycD, subgroup / Type III secretion system, low calcium response, chaperone LcrH/SycD / Tetratricopeptide repeat domain / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Tetratricopeptide-like helical domain superfamily / Mainly Alpha
Similarity search - Domain/homology
IMIDAZOLE / Chaperone protein IpgC / Type 3 secretion system translocon protein SctE
Similarity search - Component
Biological speciesShigella flexneri (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.65 Å
AuthorsLokareddy, R.K. / Lunelli, M. / Kolbe, M.
CitationJournal: J.Biol.Chem. / Year: 2010
Title: Combination of two separate binding domains defines stoichiometry between type III secretion system chaperone IpgC and translocator protein IpaB
Authors: Lokareddy, R.K. / Lunelli, M. / Eilers, B. / Wolter, V. / Kolbe, M.
History
DepositionApr 6, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 21, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 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_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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

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Assembly

Deposited unit
A: Chaperone protein ipgC
B: Chaperone protein ipgC
P: Invasin ipaB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,9776
Polymers42,7243
Non-polymers2533
Water21612
1
A: Chaperone protein ipgC
B: Chaperone protein ipgC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,6765
Polymers34,4232
Non-polymers2533
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3670 Å2
ΔGint-23 kcal/mol
Surface area14800 Å2
MethodPISA
2
P: Invasin ipaB


  • defined by author&software
  • 8.3 kDa, 1 polymers
Theoretical massNumber of molelcules
Total (without water)8,3011
Polymers8,3011
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)113.720, 113.720, 76.370
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Chaperone protein ipgC /


Mass: 17211.428 Da / Num. of mol.: 2 / Fragment: residues 1-151 / Mutation: M1G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Shigella flexneri (bacteria) / Strain: M90T / Gene: ipgC / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) RIL / References: UniProt: P0A2U4
#2: Protein Invasin ipaB / 62 kDa antigen


Mass: 8301.180 Da / Num. of mol.: 1 / Fragment: Chaperone binding regions of IpaB, residues 16-72
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Shigella flexneri (bacteria) / Strain: M90T / Gene: ipaB / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) RIL / References: UniProt: P18011
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-IMD / IMIDAZOLE / Imidazole


Mass: 69.085 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H5N2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 12 / 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: 3.34 Å3/Da / Density % sol: 63.14 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1M ADA, 1M ammonium sulfate, pH6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.91841 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Feb 6, 2008
RadiationMonochromator: Si-111 crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 2.65→35.6 Å / Num. all: 16875 / Num. obs: 15633 / % possible obs: 92.6 % / Observed criterion σ(I): -3 / Redundancy: 17.3 % / Biso Wilson estimate: 83.627 Å2 / Rmerge(I) obs: 0.069 / Net I/σ(I): 26.38
Reflection shellResolution: 2.65→2.8 Å / Redundancy: 13.6 % / Rmerge(I) obs: 0.84 / Mean I/σ(I) obs: 3.4 / Num. measured obs: 12131 / Num. unique all: 2288 / Num. unique obs: 1112 / % possible all: 90.4

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.64 Å33.42 Å
Translation2.64 Å33.42 Å

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASERphasing
REFMAC5.5.0072refinement
PDB_EXTRACT3.006data extraction
XDSdata scaling
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3GYZ

3gyz


Resolution: 2.65→35.6 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.927 / Occupancy max: 1 / Occupancy min: 1 / SU B: 31.519 / SU ML: 0.27 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.424 / ESU R Free: 0.296 / Stereochemistry target values: Engh & Huber
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS, the structure was refined also with CNS 1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.273 782 5 %RANDOM
Rwork0.233 ---
obs0.235 15633 92.7 %-
all-16864 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 121.57 Å2 / Biso mean: 79.28 Å2 / Biso min: 30.31 Å2
Baniso -1Baniso -2Baniso -3
1-2.47 Å21.23 Å20 Å2
2--2.47 Å20 Å2
3----3.7 Å2
Refinement stepCycle: LAST / Resolution: 2.65→35.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2369 0 17 12 2398
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0222433
X-RAY DIFFRACTIONr_angle_refined_deg1.8941.9623285
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4995291
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.77425.484124
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.39615415
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.732156
X-RAY DIFFRACTIONr_chiral_restr0.1210.2356
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0211861
X-RAY DIFFRACTIONr_mcbond_it0.9451.51467
X-RAY DIFFRACTIONr_mcangle_it1.84822355
X-RAY DIFFRACTIONr_scbond_it2.5283966
X-RAY DIFFRACTIONr_scangle_it4.2794.5930
LS refinement shellResolution: 2.65→2.719 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.512 55 -
Rwork0.454 1054 -
all-1109 -
obs-1109 91.8 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.2824-0.41250.36312.2347-3.25535.0201-0.18570.03440.15310.5753-0.0518-0.2495-0.74110.01780.23750.2017-0.0794-0.09950.13270.00990.08430.7504-35.63356.1594
21.3567-0.2269-0.95680.2331-0.16191.20990.00630.07450.0303-0.0101-0.0656-0.04720.01430.04910.05930.0181-0.03020.02250.15130.00670.047647.3402-54.0934-2.2599
33.4223-1.823-3.80226.99541.28174.32080.3058-0.04860.28470.0927-0.1052-0.9825-0.37980.0964-0.20060.0787-0.1023-0.02420.21230.03870.17543.1008-32.4219-1.7398
40.8833-0.40080.42160.5611-0.03150.6892-0.00630.1540.0472-0.0971-0.0524-0.0188-0.0705-0.03410.05870.0399-0.0362-0.01650.17550.04040.020320.9192-37.6203-9.0695
58.408-4.7706-0.35693.41742.44357.1064-0.4961-0.2857-1.38260.30670.19310.86750.16260.04650.3030.2758-0.0653-0.01140.18320.05440.280522.7939-44.1138-14.8538
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A8 - 32
2X-RAY DIFFRACTION2A33 - 151
3X-RAY DIFFRACTION3B9 - 32
4X-RAY DIFFRACTION4B33 - 151
5X-RAY DIFFRACTION5P64 - 70

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