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- PDB-8v5c: IpaD (122-321) Bound to Deoxycholate -

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Basic information

Entry
Database: PDB / ID: 8v5c
TitleIpaD (122-321) Bound to Deoxycholate
ComponentsInvasin IpaD
KeywordsCELL INVASION / T3SS / Shigella / Pi-helix / Deoxycholate
Function / homologyeffector-mediated activation of host programmed cell death by symbiont / Type III secretion systems tip complex components / BipD-like superfamily / Type III secretion systems tip complex components / extracellular region / Invasin IpaD
Function and homology information
Biological speciesShigella flexneri (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.96 Å
AuthorsBarker, S.A. / Dickenson, N.E. / Johnson, S.J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: J.Biol.Chem. / Year: 2024
Title: Structural and functional characterization of the IpaD pi-helix reveals critical roles in DOC interaction, T3SS apparatus maturation, and Shigella virulence.
Authors: Barker, S.A. / Bernard, A.R. / Morales, Y. / Johnson, S.J. / Dickenson, N.E.
History
DepositionNov 30, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 21, 2024Provider: repository / Type: Initial release
Revision 1.1Sep 18, 2024Group: Database references / Category: citation / Item: _citation.journal_volume

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Invasin IpaD
B: Invasin IpaD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,0166
Polymers44,0472
Non-polymers9694
Water2,756153
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4470 Å2
ΔGint-14 kcal/mol
Surface area20490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.768, 43.350, 93.439
Angle α, β, γ (deg.)90.00, 97.37, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Invasin IpaD


Mass: 22023.537 Da / Num. of mol.: 2 / Fragment: residues 122-320
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Shigella flexneri (bacteria) / Gene: ipaD / Production host: Escherichia coli (E. coli) / References: UniProt: P18013
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-DXC / (3ALPHA,5BETA,12ALPHA)-3,12-DIHYDROXYCHOLAN-24-OIC ACID / DEOXYCHOLIC ACID


Mass: 392.572 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C24H40O4 / Feature type: SUBJECT OF INVESTIGATION / Comment: detergent*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 153 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.88 Å3/Da / Density % sol: 57.24 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1 M HEPES pH 7.5, 0.018 - 0.02 M Magnesium Chloride Hexahydrate, 20% w/v Poly(acrylic acid sodium salt) 5100, 0.3 mM Deoxycholate acid sodium salt

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97946 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 15, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 1.96→35 Å / Num. obs: 35366 / % possible obs: 97.2 % / Redundancy: 6.6 % / Rmerge(I) obs: 0.095 / Rpim(I) all: 0.039 / Rrim(I) all: 0.102 / Χ2: 1.014 / Net I/σ(I): 11.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
1.96-2.035.60.33332430.9480.9870.1450.3651.03190.8
2.03-2.1160.27934790.9610.990.1190.3041.03196.5
2.11-2.216.10.22134730.9730.9930.0950.2421.05396
2.21-2.326.90.19435650.9810.9950.0780.211.02798.6
2.32-2.476.90.16535420.9810.9950.0670.1781.02698.4
2.47-2.666.90.14535980.9820.9950.0590.1571.00499.1
2.66-2.936.60.1335480.9870.9970.0540.1410.99297.4
2.93-3.357.10.11136400.9860.9960.0450.121.00999.3
3.35-4.226.70.09435640.9910.9980.0390.1020.98997.6
4.22-356.90.07837140.9940.9990.0320.0850.9998.4

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
HKL-3000data scaling
PDB_EXTRACT3.27data extraction
HKL-3000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.96→34.057 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 25.31 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2238 1762 5 %
Rwork0.1886 --
obs0.1904 35231 97.23 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.96→34.057 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2950 0 68 153 3171
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093067
X-RAY DIFFRACTIONf_angle_d1.0014156
X-RAY DIFFRACTIONf_dihedral_angle_d4.4811824
X-RAY DIFFRACTIONf_chiral_restr0.056474
X-RAY DIFFRACTIONf_plane_restr0.004524
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.96-2.0130.26311240.23892346X-RAY DIFFRACTION90
2.013-2.07220.27911320.23312520X-RAY DIFFRACTION95
2.0722-2.13910.28651330.21432523X-RAY DIFFRACTION98
2.1391-2.21550.23991320.20712513X-RAY DIFFRACTION96
2.2155-2.30420.24861360.19562592X-RAY DIFFRACTION99
2.3042-2.40910.24671380.19642613X-RAY DIFFRACTION99
2.4091-2.5360.23221380.18882617X-RAY DIFFRACTION99
2.536-2.69490.24641360.19552594X-RAY DIFFRACTION99
2.6949-2.90280.24461350.20192555X-RAY DIFFRACTION97
2.9028-3.19480.2661380.20362628X-RAY DIFFRACTION99
3.1948-3.65660.23921400.19642644X-RAY DIFFRACTION99
3.6566-4.60510.18781370.16252613X-RAY DIFFRACTION97
4.6051-34.0570.19271430.17922711X-RAY DIFFRACTION98
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)
10.64540.3277-0.45071.0593-0.90696.41510.06080.039-0.0182-0.0846-0.0845-0.0834-0.27510.42050.02660.39760.04020.01640.1942-0.01920.3439-29.9342-6.717426.6635
20.74090.026-0.1791.5664-0.00257.5122-0.00760.18430.0553-0.19510.1111-0.15860.25630.8037-0.09450.40410.03530.04590.253-0.02880.3205-24.8791-8.94813.8814
33.77992.92224.24753.54963.16827.21930.115-0.27520.15670.6283-0.23810.2744-0.2098-0.47370.17540.48220.00930.09520.1955-0.00170.3074-41.3254-19.155150.771
43.76762.28734.44371.93161.34728.34250.30430.8477-0.5726-0.4549-0.36260.62080.7736-1.3574-0.0470.65080.0861-0.20361.094-0.37590.8144-62.8582-26.290214.8217
58.4699-3.1902-1.1782.7284-3.04678.354-0.07530.0851-0.13620.41610.07430.3654-0.6878-1.42890.04240.4980.1683-0.08460.6876-0.13770.543-62.3224-15.772228.8541
61.43460.46992.27285.1467-0.60663.9284-0.19990.7878-0.152-0.41780.27340.6003-1.29510.41260.14690.98850.3256-0.2811.6645-0.39670.8444-68.9738-16.8861.4116
76.82611.14944.73352.4522.2528.49910.09231.26530.0911-0.8181-0.37320.3048-0.13620.27990.03470.57060.1296-0.03180.4198-0.03440.3329-48.3493-20.202918.637
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 122 through 186 )
2X-RAY DIFFRACTION2chain 'A' and (resid 187 through 320 )
3X-RAY DIFFRACTION3chain 'B' and (resid 123 through 149 )
4X-RAY DIFFRACTION4chain 'B' and (resid 150 through 205 )
5X-RAY DIFFRACTION5chain 'B' and (resid 206 through 250 )
6X-RAY DIFFRACTION6chain 'B' and (resid 251 through 274 )
7X-RAY DIFFRACTION7chain 'B' and (resid 275 through 319 )

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