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- PDB-5t09: The structure of the type III effector HopBA1 -

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Basic information

Entry
Database: PDB / ID: 5t09
TitleThe structure of the type III effector HopBA1
ComponentsType III secretion system effector HopBA1Type three secretion system
KeywordsTOXIN / alpha-beta fold / parallel beta core / EreA/ChaN-like
Function / homology: / Type III effector HopBA1
Function and homology information
Biological speciesPseudomonas syringae pv. aptata (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.013 Å
AuthorsCherkis, K. / Machius, M. / Nishimura, M.T. / Dangl, J.L.
Funding support United States, 3items
OrganizationGrant numberCountry
Department of Energy (DOE, United States)DE FG02 95ER20187 United States
National Science Foundation (NSF, United States)1257373 United States
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2017
Title: TIR-only protein RBA1 recognizes a pathogen effector to regulate cell death in Arabidopsis.
Authors: Nishimura, M.T. / Anderson, R.G. / Cherkis, K.A. / Law, T.F. / Liu, Q.L. / Machius, M. / Nimchuk, Z.L. / Yang, L. / Chung, E.H. / El Kasmi, F. / Hyunh, M. / Osborne Nishimura, E. / Sondek, J.E. / Dangl, J.L.
History
DepositionAug 15, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 1, 2017Provider: repository / Type: Initial release
Revision 1.1Feb 15, 2017Group: Database references
Revision 1.2Mar 22, 2017Group: Database references
Revision 1.3Sep 20, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Nov 20, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Type III secretion system effector HopBA1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,8596
Polymers25,6781
Non-polymers1815
Water46826
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)64.865, 64.865, 96.380
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 Type III secretion system effector HopBA1 / Type three secretion system


Mass: 25678.146 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas syringae pv. aptata (bacteria)
Gene: ALO85_00915 / Details (production host): N-terminal GST LIC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) Rosetta / References: UniProt: A0A0Q0CD50
#2: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#3: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 26 / 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: 2.3 Å3/Da / Density % sol: 46.53 % / Description: 120um in length
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 6uL hanging vapor diffusion drops over 0.5M K2SO4, 0.1M HEPES pH 7.0, and 30% v/v PEG 400. Protein concentration 10.7 ug/mL. 1:1 ratio protein:mother liquor

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Feb 2, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.01→32.13 Å / Num. obs: 16048 / % possible obs: 99.9 % / Redundancy: 9 % / Net I/σ(I): 49.9

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155)refinement
HKL-20002.0.0data reduction
HKL-20002.0.0data scaling
CRANK1.3.0phasing
RefinementResolution: 2.013→32.127 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.76
RfactorNum. reflection% reflection
Rfree0.2324 800 5 %
Rwork0.1999 --
obs0.2016 16016 99.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.013→32.127 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1637 0 5 26 1668
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0031671
X-RAY DIFFRACTIONf_angle_d0.5052259
X-RAY DIFFRACTIONf_dihedral_angle_d9.9371001
X-RAY DIFFRACTIONf_chiral_restr0.043247
X-RAY DIFFRACTIONf_plane_restr0.003296
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0135-2.13960.27451220.25942474X-RAY DIFFRACTION99
2.1396-2.30480.26531440.23942484X-RAY DIFFRACTION100
2.3048-2.53660.27161430.22772491X-RAY DIFFRACTION100
2.5366-2.90350.27221400.2262536X-RAY DIFFRACTION100
2.9035-3.65730.25621290.22392550X-RAY DIFFRACTION100
3.6573-32.13070.19211220.16912681X-RAY DIFFRACTION100
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)
16.2707-0.0631.35184.63030.08022.1818-0.34360.67031.2927-0.49880.1087-0.3806-0.52570.31330.15030.3703-0.0641-0.02790.51550.14430.481714.334738.560524.372
28.31161.2317.24396.6559-1.93557.71510.08922.3483-1.6136-1.58780.312-0.95680.73781.3824-0.64060.52560.0530.08410.6719-0.18380.677912.575517.063921.91
37.0808-4.1305-0.15523.84452.67587.2881-0.01850.0001-1.53520.34450.34540.58221.335-0.73550.13310.2718-0.1159-0.03410.476-0.02010.5191.813321.288327.0474
46.1794-0.3210.53882.67020.99450.4304-0.0040.304-0.109-0.26930.0140.09960.3922-0.03270.06460.332-0.04220.05710.5107-0.04370.41547.702925.531428.8873
56.4563-0.32450.77725.52862.1273.0092-0.07710.1569-0.3880.1111-0.1782-0.03410.0202-0.51080.20890.18730.0429-0.0750.38470.00680.332415.062927.502540.2953
65.1124-1.35391.09244.2014-0.70022.9165-0.7062-0.14941.67310.22870.1805-0.724-0.81680.257-0.05850.41520.0088-0.12240.4419-0.03380.657213.339841.247632.9369
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 23 through 86 )
2X-RAY DIFFRACTION2chain 'A' and (resid 87 through 100 )
3X-RAY DIFFRACTION3chain 'A' and (resid 101 through 116 )
4X-RAY DIFFRACTION4chain 'A' and (resid 117 through 151 )
5X-RAY DIFFRACTION5chain 'A' and (resid 152 through 180 )
6X-RAY DIFFRACTION6chain 'A' and (resid 181 through 239 )

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