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- PDB-5vxm: 2.05 A resolution structure of IpaD from Shigella flexneri in com... -

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Basic information

Entry
Database: PDB / ID: 5vxm
Title2.05 A resolution structure of IpaD from Shigella flexneri in complex with single-domain antibody 20ipaD
Components
  • Invasin IpaD
  • Single-domain antibody 20ipaD
KeywordsIMMUNE SYSTEM / tip protein / VHH / T3SS
Function / homology
Function and homology information


effector-mediated activation of programmed cell death in host / 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 / molecular replacement / Resolution: 2.05 Å
AuthorsBarta, M.L. / Lovell, S. / Battaile, K.P. / Picking, W.D. / Picking, W.L.
CitationJournal: To Be Published
Title: 2.05 A resolution structure of IpaD from Shigella flexneri in complex with single-domain antibody 20ipaD
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 20ipaD


Theoretical massNumber of molelcules
Total (without water)48,1592
Polymers48,1592
Non-polymers00
Water1,22568
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)58.642, 83.507, 181.609
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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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 20ipaD


Mass: 16253.950 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.: 68 / 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: 2.31 Å3/Da / Density % sol: 46.72 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 3.5 / Details: 0.1 M Citric acid (pH 3.5), 25 % (w/v) PEG 3350

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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: 2.05→47.99 Å / Num. obs: 28469 / % possible obs: 99.9 % / Redundancy: 6.4 % / Biso Wilson estimate: 38.31 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.078 / Rpim(I) all: 0.033 / Rrim(I) all: 0.085 / Net I/σ(I): 13 / Num. measured all: 182091 / Scaling rejects: 16
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.05-2.116.51.0361432521910.6370.4391.1271.9100
8.94-47.995.60.03822103980.9980.0170.04236.398.3

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIXdev_2846refinement
Aimless0.5.27data scaling
PDB_EXTRACT3.22data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2J0O

2j0o


Resolution: 2.05→34.371 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.43 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2463 1356 4.77 %
Rwork0.2099 27059 -
obs0.2117 28415 99.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 194.82 Å2 / Biso mean: 62.941 Å2 / Biso min: 23.99 Å2
Refinement stepCycle: final / Resolution: 2.05→34.371 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2690 0 0 68 2758
Biso mean---49.86 -
Num. residues----368
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0022728
X-RAY DIFFRACTIONf_angle_d0.4573705
X-RAY DIFFRACTIONf_chiral_restr0.036437
X-RAY DIFFRACTIONf_plane_restr0.002479
X-RAY DIFFRACTIONf_dihedral_angle_d11.3771629
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 10 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.05-2.12330.34861510.285926732824
2.1233-2.20830.27011220.260326562778
2.2083-2.30870.24041240.244426852809
2.3087-2.43040.28351300.22826982828
2.4304-2.58270.2721500.228126432793
2.5827-2.7820.2521110.226127282839
2.782-3.06180.28881300.222826972827
3.0618-3.50450.2451440.202727022846
3.5045-4.41380.19941610.182727182879
4.4138-34.37570.25091330.199328592992
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)
10.1872-0.0658-0.29040.36580.02960.2279-0.1358-0.2427-0.03560.0347-0.13220.1931-0.1761-0.0063-0.43390.6130.1401-0.05770.6845-0.21210.3014-10.53196.2985-6.4541
20.934-0.32910.0820.6202-0.21240.5502-0.0238-0.01270.06710.0287-0.003-0.192-0.0758-0.1209-00.2834-0.0353-0.02040.2508-0.00110.28232.0243-3.7483-28.5622
30.24620.04140.18580.2145-0.13640.245-0.3901-0.1235-0.07530.2121-0.3260.1520.1664-0.131-0.01050.376-0.10450.04370.3939-0.00630.4378-13.0553-37.8903-30.3725
40.0084-0.0128-0.01230.00690.00920.0125-0.1658-0.0928-0.47280.0989-0.18510.28440.02440.1028-0.00050.4284-0.10460.01590.47110.0110.3601-5.4557-23.6673-20.9276
50.02110.0293-0.0538-0.00560.01330.1345-0.0391-0.0924-0.7398-0.0817-0.3348-0.853-0.08050.0788-0.00920.3561-0.06850.00230.2980.08220.6986-1.3386-38.0021-34.5515
60.00930.0826-0.08670.0349-0.0161-0.04590.0875-0.11890.1285-0.1839-0.16-0.0994-0.15850.0711-0.00010.2875-0.0259-0.0150.3333-0.02650.3503-5.6224-23.9276-34.4255
70.30850.10490.07490.2344-0.10480.0623-0.01870.05070.01350.09010.01150.2173-0.6177-0.1255-0.00070.3077-0.0148-0.00730.374-0.00050.2668-11.7909-28.9943-34.23
80.16470.0973-0.056-0.0042-0.05640.0441-0.25950.0243-0.3013-0.1048-0.1086-0.3297-0.12140.1696-0.00190.2992-0.05820.03530.296-0.00140.3236-7.3217-37.9335-37.4278
90.01030.01780.03090.03350.01130.01440.2419-0.2146-0.53950.2618-0.4737-0.06820.04-0.1747-00.3677-0.0623-0.09350.277-0.00030.37742.0267-22.8328-31.3311
100.017-0.0308-0.16530.62420.13510.44790.0132-0.1593-0.48080.1043-0.234-0.87320.0805-0.2132-0.06090.3041-0.0979-0.01190.30230.05760.5408-3.4878-38.4948-32.3806
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 42 through 149 )A42 - 149
2X-RAY DIFFRACTION2chain 'A' and (resid 150 through 320 )A150 - 320
3X-RAY DIFFRACTION3chain 'B' and (resid 2 through 25 )B2 - 25
4X-RAY DIFFRACTION4chain 'B' and (resid 26 through 33 )B26 - 33
5X-RAY DIFFRACTION5chain 'B' and (resid 34 through 45 )B34 - 45
6X-RAY DIFFRACTION6chain 'B' and (resid 46 through 60 )B46 - 60
7X-RAY DIFFRACTION7chain 'B' and (resid 61 through 83 )B61 - 83
8X-RAY DIFFRACTION8chain 'B' and (resid 84 through 99 )B84 - 99
9X-RAY DIFFRACTION9chain 'B' and (resid 100 through 108 )B100 - 108
10X-RAY DIFFRACTION10chain 'B' and (resid 109 through 126 )B109 - 126

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