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- PDB-3gz1: Crystal structure of IpgC in complex with the chaperone binding r... -

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Basic information

Entry
Database: PDB / ID: 3gz1
TitleCrystal structure of IpgC in complex with the chaperone binding region of IpaB
Components
  • Chaperone protein ipgC
  • Invasin ipaB
KeywordsCHAPERONE / Tetratricopeptide repeat / TPR / chaperone binding region / Virulence / Membrane / Secreted / Transmembrane
Function / homology
Function and homology information


host cell membrane / host cell / host cell nucleus / extracellular region / identical protein binding / membrane / 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
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: 2.15 Å
AuthorsLunelli, M. / Lokareddy, R.K. / Zychlinsky, A. / Kolbe, M.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2009
Title: IpaB-IpgC interaction defines binding motif for type III secretion translocator
Authors: Lunelli, M. / Lokareddy, R.K. / Zychlinsky, A. / Kolbe, M.
History
DepositionApr 6, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 16, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Jan 27, 2021Group: Data collection / Derived calculations / Source and taxonomy
Category: diffrn / pdbx_entity_src_syn ...diffrn / pdbx_entity_src_syn / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / struct_site
Item: _pdbx_entity_src_syn.ncbi_taxonomy_id / _pdbx_entity_src_syn.organism_scientific ..._pdbx_entity_src_syn.ncbi_taxonomy_id / _pdbx_entity_src_syn.organism_scientific / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 10, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Nov 1, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)39,4047
Polymers39,1284
Non-polymers2763
Water1,15364
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)73.310, 97.090, 106.530
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 Chaperone protein ipgC


Mass: 17211.428 Da / Num. of mol.: 2 / Fragment: UNP residues 1-151
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/peptide Invasin ipaB / 62 kDa antigen


Mass: 2352.663 Da / Num. of mol.: 2
Fragment: Chaperone binding region of IpaB, UNP residues 51-72
Source method: obtained synthetically / Details: synthesized peptide / Source: (synth.) Shigella flexneri (bacteria) / References: UniProt: P18011
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 64 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.42 Å3/Da / Density % sol: 49.22 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: 0.1M HEPES, 20% PEG 8000, 8% ethylene glycol, pH7.4, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONBESSY 14.210.91841
SYNCHROTRONBESSY 14.120.91841
Detector
TypeIDDetectorDate
MAR CCD 165 mm1CCDAug 9, 2007
MARMOSAIC 225 mm CCD2CCDNov 21, 2007
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Si-111 crystalSINGLE WAVELENGTHMx-ray1
2Si-111 crystalSINGLE WAVELENGTHMx-ray1
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 2.15→39.37 Å / Num. all: 21045 / Num. obs: 19676 / % possible obs: 93.5 % / Observed criterion σ(I): -3 / Redundancy: 8.7 % / Biso Wilson estimate: 52.712 Å2 / Rmerge(I) obs: 0.154 / Net I/σ(I): 13.17
Reflection shellResolution: 2.15→2.21 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.68 / Mean I/σ(I) obs: 2 / Num. measured obs: 6125 / Num. unique all: 1316 / Num. unique obs: 1316 / % possible all: 86.5

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å35.85 Å
Translation2.5 Å35.85 Å

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASERphasing
REFMAC5.5.0044refinement
PDB_EXTRACT3.006data extraction
XDSdata scaling
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3GYZ

3gyz


Resolution: 2.15→39.37 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.937 / Occupancy max: 1 / Occupancy min: 1 / SU B: 13.603 / SU ML: 0.153 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.241 / ESU R Free: 0.186 / 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
Rfree0.23 983 5 %RANDOM
Rwork0.2 ---
obs0.201 19676 93.5 %-
all-21043 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 94.2 Å2 / Biso mean: 49.861 Å2 / Biso min: 23.75 Å2
Baniso -1Baniso -2Baniso -3
1-3.02 Å20 Å20 Å2
2---0.69 Å20 Å2
3----2.32 Å2
Refinement stepCycle: LAST / Resolution: 2.15→39.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2483 0 18 64 2565
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.0222548
X-RAY DIFFRACTIONr_angle_refined_deg2.0691.9713440
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.365305
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.0925.52125
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.70715441
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.96156
X-RAY DIFFRACTIONr_chiral_restr0.1570.2376
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0211932
X-RAY DIFFRACTIONr_mcbond_it1.3431.51545
X-RAY DIFFRACTIONr_mcangle_it2.44722483
X-RAY DIFFRACTIONr_scbond_it3.53831003
X-RAY DIFFRACTIONr_scangle_it5.8634.5957
LS refinement shellResolution: 2.15→2.206 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.313 65 -
Rwork0.293 1247 -
all-1312 -
obs-1312 86.6 %
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)
10.47321.0601-0.59285.1688-1.77030.81670.16090.16870.0918-0.32550.08421.1105-0.071-0.1865-0.24510.23560.0576-0.18060.2333-0.07450.3113-38.812122.7692-0.8064
20.5518-0.4366-0.72680.91440.59511.3409-0.03420.02310.0205-0.1707-0.0150.0679-0.0081-0.03410.04920.0824-0.0086-0.03490.06950.00440.0314-23.174137.5059-13.8216
38.01031.4726-4.4710.429-1.17334.4101-0.15021.00050.1277-0.27230.20170.08240.3603-0.2893-0.05150.4425-0.1126-0.12810.20640.06060.0432-34.017915.085-14.0269
40.15250.20860.00081.0804-1.21021.8932-0.0374-0.0112-0.0133-0.0993-0.0333-0.06890.11110.05790.07070.05840.0060.00530.0591-0.00230.0071-26.388914.26587.9273
52.0860.1313-1.93030.64571.57848.72090.2287-0.2104-0.00340.0720.0629-0.2895-0.11350.4921-0.29160.04210.0093-0.02940.1060.00690.2321-17.609317.41847.4878
60.23640.0231.07539.1468-0.39824.95540.04760.0041-0.095-0.85070.3465-0.08420.2854-0.0859-0.39410.208-0.0328-0.03240.2159-0.09470.0823-29.718243.4545-17.8906
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A8 - 32
2X-RAY DIFFRACTION2A33 - 151
3X-RAY DIFFRACTION3B10 - 32
4X-RAY DIFFRACTION4B33 - 151
5X-RAY DIFFRACTION5P60 - 72
6X-RAY DIFFRACTION6Q63 - 72

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