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- PDB-5vxl: 2.80 A resolution structure of IpaD from Shigella flexneri in com... -

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Basic information

Entry
Database: PDB / ID: 5vxl
Title2.80 A resolution structure of IpaD from Shigella flexneri in complex with single-domain antibody JPS-G3
Components
  • Invasin IpaD
  • single-domain antibody JPS-G3
KeywordsIMMUNE SYSTEM / tip protein / VHH / T3SS
Function / homology
Function and homology information


effector-mediated activation of host programmed cell death by symbiont / extracellular region
Similarity search - Function
IpaD-like / IpaD-like / Type III secretion systems tip complex components / BipD-like superfamily / Type III secretion systems tip complex components / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesShigella flexneri (bacteria)
Vicugna pacos (alpaca)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsBarta, M.L. / Lovell, S. / Battaile, K.P. / Picking, W.D. / Picking, W.L.
CitationJournal: To Be Published
Title: 2.80 A resolution structure of IpaD from Shigella flexneri in complex with single-domain antibody JPS-G3
Authors: Barta, M.L. / Lovell, S. / Battaile, K.P. / Picking, W.D. / Picking, W.L.
History
DepositionMay 23, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 30, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 4, 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: Invasin IpaD
B: single-domain antibody JPS-G3


Theoretical massNumber of molelcules
Total (without water)47,5822
Polymers47,5822
Non-polymers00
Water1267
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)55.779, 81.572, 92.906
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Invasin IpaD / 36 kDa membrane antigen


Mass: 31904.623 Da / Num. of mol.: 1 / Mutation: C322S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Shigella flexneri (bacteria) / Gene: ipaD, CP0126 / Production host: Escherichia coli (E. coli) / References: UniProt: P18013
#2: Antibody single-domain antibody JPS-G3


Mass: 15677.406 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vicugna pacos (alpaca) / Production host: Escherichia coli (E. coli)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 7 / 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: 2.22 Å3/Da / Density % sol: 44.62 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.2 M Lithium sulfate, 0.1 M Tris-HCl (pH 8.5), 30% (w/v) PEG 4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 14, 2016
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→47.82 Å / Num. obs: 10958 / % possible obs: 100 % / Redundancy: 6.5 % / Biso Wilson estimate: 42.76 Å2 / CC1/2: 0.992 / Rmerge(I) obs: 0.204 / Rpim(I) all: 0.086 / Rrim(I) all: 0.222 / Net I/σ(I): 8.8 / Num. measured all: 71018 / Scaling rejects: 0
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Rpim(I) allRrim(I) all% possible all
2.8-2.956.41.0940.6990.4621.19100
8.85-47.825.50.0480.9980.0210.05299.7

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Processing

Software
NameVersionClassification
Aimless0.5.27data scaling
PHENIXdev_2775refinement
PDB_EXTRACT3.22data extraction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2J0O

2j0o


Resolution: 2.8→47.82 Å / SU ML: 0.45 / Cross valid method: FREE R-VALUE / σ(F): 0.17 / Phase error: 28.42
RfactorNum. reflection% reflection
Rfree0.2731 980 4.88 %
Rwork0.2017 --
obs0.2053 20098 99.62 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 160.16 Å2 / Biso mean: 51.0579 Å2 / Biso min: 4.29 Å2
Refinement stepCycle: final / Resolution: 2.8→47.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2985 0 0 7 2992
Biso mean---21.94 -
Num. residues----391
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023030
X-RAY DIFFRACTIONf_angle_d0.4194109
X-RAY DIFFRACTIONf_chiral_restr0.036475
X-RAY DIFFRACTIONf_plane_restr0.002529
X-RAY DIFFRACTIONf_dihedral_angle_d10.8241831
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.8002-2.94780.32031430.28722728287199
2.9478-3.13240.35471490.266327172866100
3.1324-3.37420.32691130.238827522865100
3.3742-3.71370.26291620.227292891100
3.7137-4.25080.25251270.159227582885100
4.2508-5.35440.23391380.160427162854100
5.3544-47.8290.25721480.20732718286699
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)
10.0257-0.0702-0.00410.1514-0.12010.0442-0.01970.0443-0.083-0.02490.0039-0.0644-0.0469-0.0851-0.00250.2850.0339-0.04330.280.05780.211215.127685.743955.33
20.14370.05630.02410.0722-0.20540.074-0.11920.0199-0.0460.05410.05630.07650.0125-0.0832-0.030.14210.03560.01420.17820.03860.18376.1046100.876125.0073
3-0.05020.02-0.0431-0.0398-0.10130.0722-0.02140.0485-0.00840.0327-0.0812-0.10520.0223-0.0022-0.01920.251-0.0202-0.06630.15360.01960.21916.4285101.7938.0521
40.0044-0.0038-0.00230.00120.0020.0049-0.06820.03820.0287-0.12140.0796-0.00470.09730.051300.1324-0.05510.01240.2299-0.05430.208112.15484.93562.2243
50.0068-0.00240.0040.0013-0.0010.0034-0.0345-0.00080.1060.06280.0630.0080.03310.0306-00.2120.0641-0.0770.1950.0110.190728.43568.30627.4089
60.02110.0653-0.06910.1067-0.10950.16030.02510.1105-0.0972-0.11850.102-0.01360.1481-0.01250.03580.16150.0471-0.03950.1637-0.06720.192514.202883.02169.7211
71.0775-0.0196-0.210.1035-0.15140.2595-0.1716-0.0264-0.20610.0729-0.0722-0.0754-0.0943-0.146-0.40370.24490.1043-0.17560.1952-0.01950.169611.491177.182715.3348
80.05020.0039-0.00710.07840.04720.03520.08490.02-0.07220.2854-0.0948-0.12770.10990.14290.03820.21720.087-0.02440.2116-0.02840.154319.505980.52115.749
90.02250.0135-0.06380.0647-0.05270.19530.1038-0.11-0.061-0.06090.0292-0.02450.0356-0.10.21170.1310.0324-0.06880.1301-0.04130.168614.308374.69168.7596
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 40 through 149 )A40 - 149
2X-RAY DIFFRACTION2chain 'A' and (resid 150 through 272 )A150 - 272
3X-RAY DIFFRACTION3chain 'A' and (resid 273 through 322 )A273 - 322
4X-RAY DIFFRACTION4chain 'B' and (resid 1 through 7 )B1 - 7
5X-RAY DIFFRACTION5chain 'B' and (resid 8 through 17 )B8 - 17
6X-RAY DIFFRACTION6chain 'B' and (resid 18 through 39 )B18 - 39
7X-RAY DIFFRACTION7chain 'B' and (resid 40 through 58 )B40 - 58
8X-RAY DIFFRACTION8chain 'B' and (resid 59 through 84 )B59 - 84
9X-RAY DIFFRACTION9chain 'B' and (resid 85 through 116 )B85 - 116

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