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- PDB-3gyz: Crystal structure of IpgC from Shigella flexneri -

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Basic information

Entry
Database: PDB / ID: 3gyz
TitleCrystal structure of IpgC from Shigella flexneri
ComponentsChaperone protein ipgC
KeywordsCHAPERONE / asymmetric homodimer / Tetratricopeptide repeat / TPR / Virulence
Function / homology
Function and homology information


identical protein binding / cytoplasm
Similarity search - Function
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
Similarity search - Component
Biological speciesShigella flexneri (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / 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 1.2Nov 10, 2021Group: Database references / Derived calculations / Category: database_2 / 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
Revision 1.3May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,28312
Polymers34,4232
Non-polymers86010
Water1,54986
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4930 Å2
ΔGint-62 kcal/mol
Surface area14680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)115.150, 115.150, 75.460
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: 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: Chemical ChemComp-SO4 / SULFATE ION


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


Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 86 / 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: 4.2 Å3/Da / Density % sol: 70.68 %
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

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
1,21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONESRF ID23-110.97625
SYNCHROTRONBESSY 14.220.97965, 0.97987, 0.97626, 0.98793
Detector
TypeIDDetectorDate
ADSC QUANTUM 315r1CCDMay 14, 2007
MAR CCD 165 mm2CCDApr 25, 2007
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Silicon (1 1 1) channel-cutSINGLE WAVELENGTHMx-ray1
2Si-111 crystalMADMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.976251
20.979651
30.979871
40.976261
50.987931
ReflectionNumber: 71688 / Rmerge(I) obs: 0.104 / D res high: 3.1 Å / Num. obs: 19973 / % possible obs: 99.5
ReflectionResolution: 2.15→37.69 Å / Num. all: 31712 / Num. obs: 31628 / % possible obs: 99.735 % / Observed criterion σ(I): -3 / Redundancy: 9.1 % / Biso Wilson estimate: 55.242 Å2 / Rmerge(I) obs: 0.125 / Net I/σ(I): 10.12
Reflection shellResolution: 2.15→2.28 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.548 / Mean I/σ(I) obs: 2.1 / Num. measured obs: 17987 / Num. unique all: 4963 / Num. unique obs: 4963 / % possible all: 98.7

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
SHARPphasing
SOLOMONphasing
REFMAC5.5.0044refinement
PDB_EXTRACT3.006data extraction
XDSdata scaling
XDSdata reduction
RefinementMethod to determine structure: MAD / Resolution: 2.15→37.69 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.956 / Occupancy max: 1 / Occupancy min: 1 / SU B: 9.023 / SU ML: 0.103 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.145 / ESU R Free: 0.133 / 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
Rfree0.214 1577 5 %RANDOM
Rwork0.191 ---
obs0.192 31628 99.735 %-
all-31712 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 92.45 Å2 / Biso mean: 46.163 Å2 / Biso min: 27.81 Å2
Baniso -1Baniso -2Baniso -3
1-0.16 Å20.08 Å20 Å2
2--0.16 Å20 Å2
3----0.23 Å2
Refinement stepCycle: LAST / Resolution: 2.15→37.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2308 0 53 86 2447
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.0222399
X-RAY DIFFRACTIONr_angle_refined_deg1.9381.9693233
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0735284
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.28625.41122
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.64315404
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.027156
X-RAY DIFFRACTIONr_chiral_restr0.1260.2346
X-RAY DIFFRACTIONr_gen_planes_refined0.010.021812
X-RAY DIFFRACTIONr_mcbond_it1.2521.51426
X-RAY DIFFRACTIONr_mcangle_it2.36522288
X-RAY DIFFRACTIONr_scbond_it3.873973
X-RAY DIFFRACTIONr_scangle_it6.3334.5945
LS refinement shellResolution: 2.151→2.207 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.328 118 -
Rwork0.324 2176 -
all-2294 -
obs-2294 97.3 %
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)
12.2993-0.50372.69570.2214-0.74893.4188-0.2526-0.31980.22760.0049-0.0047-0.0408-0.1393-0.30850.25730.21220.016-0.01140.0882-0.04710.116247.1798.04619.132
20.75380.7285-0.45390.8282-0.52580.7031-0.10210.00820.0487-0.05530.0227-0.01290.04020.0830.07950.1687-0.0681-0.01450.07980.03730.127370.96114.07610.149
38.60353.2121-3.00382.1724-2.23144.390.1234-0.36011.9015-0.024-0.14050.3799-0.74430.26630.0170.335-0.0489-0.06040.0225-0.05670.574149.72120.85810.511
41.03220.21460.54190.61160.6520.8010.04390.01940.0660.0656-0.10070.0330.0521-0.08080.05680.1776-0.0731-0.00670.04680.00260.062843.549-1.1653.42
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A9 - 32
2X-RAY DIFFRACTION2A33 - 151
3X-RAY DIFFRACTION3B9 - 32
4X-RAY DIFFRACTION4B33 - 151

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