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- PDB-6pwd: Ewingella americana HopBF1 kinase -

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Basic information

Entry
Database: PDB / ID: 6pwd
TitleEwingella americana HopBF1 kinase
ComponentsType III effector HopBF1
KeywordsTRANSFERASE / HSP90 / phosphorylation / chaperone / immunity / kinase
Function / homologyType III effector HopBF1 / Type III effector HopBF1
Function and homology information
Biological speciesEwingella americana (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.47 Å
AuthorsTomchick, D.R. / Tagliabracci, V.S. / Park, B.C.
Funding support United States, Poland, 5items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Dental and Craniofacial Research (NIH/NIDCR)R00DK099254 United States
Robert A. Welch FoundationI-1911 United States
Cancer Prevention and Research Institute of Texas (CPRIT)RP170674 United States
Polish National Science Centre2014/15/B/NZ1/03559 Poland
Polish National Science Centre2017/25/B/NZ1/01883 Poland
CitationJournal: Cell / Year: 2019
Title: A Bacterial Effector Mimics a Host HSP90 Client to Undermine Immunity.
Authors: Lopez, V.A. / Park, B.C. / Nowak, D. / Sreelatha, A. / Zembek, P. / Fernandez, J. / Servage, K.A. / Gradowski, M. / Hennig, J. / Tomchick, D.R. / Pawlowski, K. / Krzymowska, M. / Tagliabracci, V.S.
History
DepositionJul 22, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 11, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 2, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: Type III effector HopBF1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,0698
Polymers22,6001
Non-polymers4687
Water39622
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)134.953, 134.953, 124.489
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32
Space group name HallR32"
Symmetry operation#1: x,y,z
#2: -y,x-y,z
#3: -x+y,-x,z
#4: x-y,-y,-z
#5: -x,-x+y,-z
#6: y,x,-z
#7: x+1/3,y+2/3,z+2/3
#8: -y+1/3,x-y+2/3,z+2/3
#9: -x+y+1/3,-x+2/3,z+2/3
#10: x-y+1/3,-y+2/3,-z+2/3
#11: -x+1/3,-x+y+2/3,-z+2/3
#12: y+1/3,x+2/3,-z+2/3
#13: x+2/3,y+1/3,z+1/3
#14: -y+2/3,x-y+1/3,z+1/3
#15: -x+y+2/3,-x+1/3,z+1/3
#16: x-y+2/3,-y+1/3,-z+1/3
#17: -x+2/3,-x+y+1/3,-z+1/3
#18: y+2/3,x+1/3,-z+1/3

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Components

#1: Protein Type III effector HopBF1


Mass: 22600.324 Da / Num. of mol.: 1 / Mutation: N-terminal S from purification tag
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ewingella americana (bacteria) / Gene: A8A01_18940 / Plasmid: ppSumo / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta / References: UniProt: A0A2N0N2I2, UniProt: A0A085GHR3*PLUS
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 22 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 4.83 Å3/Da / Density % sol: 74.5 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 1.4 M ammonium sulfate, 0.1 M sodium citrate, 0.2 M sodium potassium tartrate, 0.05 M sodium chloride, 25% ethylene glycol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 1.007 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Feb 16, 2017 / Details: monochromator
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.007 Å / Relative weight: 1
ReflectionResolution: 2.47→42.6 Å / Num. obs: 15724 / % possible obs: 100 % / Redundancy: 18.1 % / Biso Wilson estimate: 34.22 Å2 / Rmerge(I) obs: 0.054 / Rpim(I) all: 0.013 / Net I/σ(I): 55.8
Reflection shellResolution: 2.47→2.51 Å / Redundancy: 16.4 % / Rmerge(I) obs: 1.208 / Mean I/σ(I) obs: 2.6 / Num. unique obs: 770 / CC1/2: 0.8 / Rpim(I) all: 0.304 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-3000data reduction
PHENIX1.16_3549refinement
HKL-3000data scaling
PHENIXphasing
Cootmodel building
RefinementMethod to determine structure: SAD / Resolution: 2.47→42.6 Å / SU ML: 0.2441 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.6415
RfactorNum. reflection% reflectionSelection details
Rfree0.2175 1555 9.99 %random
Rwork0.2019 ---
obs0.2035 15558 98.99 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 47.37 Å2
Refinement stepCycle: LAST / Resolution: 2.47→42.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1382 0 29 22 1433
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00231428
X-RAY DIFFRACTIONf_angle_d0.55641919
X-RAY DIFFRACTIONf_chiral_restr0.0441216
X-RAY DIFFRACTIONf_plane_restr0.0029254
X-RAY DIFFRACTIONf_dihedral_angle_d12.703872
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.47-2.550.2961250.25541126X-RAY DIFFRACTION89.23
2.55-2.650.24841410.23111273X-RAY DIFFRACTION99.58
2.65-2.750.25011410.2241265X-RAY DIFFRACTION100
2.75-2.880.24661400.22971268X-RAY DIFFRACTION100
2.88-3.030.24281420.22481268X-RAY DIFFRACTION99.93
3.03-3.220.2571420.23411288X-RAY DIFFRACTION100
3.22-3.470.24981430.22571284X-RAY DIFFRACTION100
3.47-3.810.20591430.19811283X-RAY DIFFRACTION100
3.81-4.370.17441440.1631298X-RAY DIFFRACTION100
4.37-5.50.17471440.15061293X-RAY DIFFRACTION100
5.5-42.60.2071500.21411357X-RAY DIFFRACTION99.93
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)
12.11112973834-0.3244893421110.9089952238544.24470878621-2.191162049734.62964022852-0.1939595840870.005298861420510.07161661431030.4056783088640.2671658722450.794233643628-0.1159654214290.0498179784463-0.02813826519650.4444241994760.1033012672120.1072549179840.2224134852620.09901183820280.356642588189-15.044651233931.937277640348.0719604452
21.59305195181-1.920433852010.2690149612194.2703324573-0.106219595461.42230399183-0.1323649519890.1108719158870.313682581176-0.08312294622820.3532458163410.4495698811530.0033906248987-0.10371820642-0.1472268879410.4229658429650.008268320424150.05584786867810.2168596249630.1175767724740.365605033235-10.199034615523.521447320643.9612689423
34.790151859180.07688885104590.8459654570813.699726901730.3113288817832.63453823035-0.05925103545630.662903980456-0.101988282386-0.7340784505380.12144064087-0.3064618868740.1394889522770.228591930034-0.07484614674410.5487109671680.0671899473010.1227453001710.291682751270.01166513728420.264495411362-0.92908752685914.504531826538.3911847843
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 25 through 67 )
2X-RAY DIFFRACTION2chain 'A' and (resid 68 through 128 )
3X-RAY DIFFRACTION3chain 'A' and (resid 129 through 200 )

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