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- PDB-6pwg: Ewingella americana HopBF1 kinase bound to AMP-PNP -

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Basic information

Entry
Database: PDB / ID: 6pwg
TitleEwingella americana HopBF1 kinase bound to AMP-PNP
ComponentsType III effector HopBF1
KeywordsTRANSFERASE / HSP90 / phosphorylation / chaperone / immunity / kinase
Function / homologyPHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / Type III effector HopBF1 / Type III effector HopBF1
Function and homology information
Biological speciesEwingella americana (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.89 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 23, 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 1.3Oct 11, 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

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Assembly

Deposited unit
A: Type III effector HopBF1
B: Type III effector HopBF1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,5239
Polymers45,2012
Non-polymers1,3237
Water4,179232
1
A: Type III effector HopBF1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,3556
Polymers22,6001
Non-polymers7545
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Type III effector HopBF1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,1693
Polymers22,6001
Non-polymers5682
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)76.185, 76.185, 351.362
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
Components on special symmetry positions
IDModelComponents
11A-524-

HOH

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Components

#1: Protein Type III effector HopBF1


Mass: 22600.324 Da / Num. of mol.: 2
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-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 232 / 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: 2.17 Å3/Da / Density % sol: 43.34 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 0.2 M sodium citrate, 22% PEG3000, 1 mM AMP-PNP, 5 mM manganese chloride, 1 mM TCEP, 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: Apr 18, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.007 Å / Relative weight: 1
ReflectionResolution: 1.89→36.22 Å / Num. obs: 31760 / % possible obs: 99.7 % / Redundancy: 3.8 % / Biso Wilson estimate: 20.2 Å2 / Rmerge(I) obs: 0.07 / Rpim(I) all: 0.04 / Net I/σ(I): 11.5
Reflection shellResolution: 1.89→1.93 Å / Redundancy: 3.7 % / Rmerge(I) obs: 1.212 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 1546 / CC1/2: 0.79 / Rpim(I) all: 0.728 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6PWD

6pwd


Resolution: 1.89→36.22 Å / SU ML: 0.2081 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.6701
RfactorNum. reflection% reflection
Rfree0.241 1996 6.72 %
Rwork0.2056 --
obs0.2079 29703 92.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 29.09 Å2
Refinement stepCycle: LAST / Resolution: 1.89→36.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2748 0 82 232 3062
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00742884
X-RAY DIFFRACTIONf_angle_d0.81593905
X-RAY DIFFRACTIONf_chiral_restr0.0512441
X-RAY DIFFRACTIONf_plane_restr0.0045510
X-RAY DIFFRACTIONf_dihedral_angle_d12.50981754
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.89-1.940.3630.269864X-RAY DIFFRACTION41.51
1.94-1.990.28221100.26261532X-RAY DIFFRACTION73.21
1.99-2.050.27781380.2411926X-RAY DIFFRACTION91.61
2.05-2.120.29471510.22962087X-RAY DIFFRACTION98.72
2.12-2.190.26951500.22012080X-RAY DIFFRACTION99.64
2.19-2.280.23371510.20142085X-RAY DIFFRACTION99.78
2.28-2.390.25791520.2012122X-RAY DIFFRACTION99.78
2.39-2.510.26061510.20162091X-RAY DIFFRACTION99.78
2.51-2.670.2331530.19052127X-RAY DIFFRACTION99.69
2.67-2.880.25071530.20242112X-RAY DIFFRACTION99.74
2.88-3.160.24031550.19382139X-RAY DIFFRACTION99.65
3.16-3.620.20071530.18442137X-RAY DIFFRACTION99.39
3.62-4.560.19151550.17232158X-RAY DIFFRACTION99.23
4.56-36.220.27411610.24182247X-RAY DIFFRACTION97.85
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)
12.42731712350.0835900552160.49025099064.570762831510.3144176426562.835154825330.09688166484360.362449765014-0.256710356187-0.309922319275-0.145812130123-0.3063255034420.4457763243340.3844022859450.0125997337890.2362615762210.127101075310.0004006578576390.253053322081-0.0714644677350.22076239936424.590832391217.6892587508-18.7980557279
28.32688646952-4.747303898693.751094739353.35608677078-1.874665813792.613540778270.09566830193670.0168920126816-0.7182377344540.06661403744970.03489554297960.5389839655320.4001431869280.0945245426533-0.1326622068510.1783882235470.04916446483050.03011541230990.173222647655-0.002930330197640.26392049595611.057600096318.9125896499-12.4618033149
32.07596664814-2.089730096250.2128708755024.194714548150.02924050924150.9828945158740.252788349579-0.0419959070954-0.285955672528-0.4098707174780.03815894424590.164661304770.3031404695430.118653860078-0.2335246804410.1800454373350.0316942693428-0.05507151727810.152887877896-0.03931304318460.17834032221213.741628061221.8478548059-18.7073275101
41.79038255338-0.12613406208-0.04904658924495.278367466940.6833113168920.8440664490210.04188530567210.2226284017350.08217334134630.1455663739770.0481577010195-0.4259745987280.2059771374850.371424687859-0.005938954912120.1147834373830.0515313382111-0.03013164507190.1921754484280.00675521517410.15948826662323.206202447327.2275825083-16.9036171568
53.56762254783-2.503411151983.978660516463.98526828872-0.5971878088646.88192525033-0.169863887846-0.3751178511530.7896959665090.2622817644230.040700851017-1.28548205077-0.278659266503-0.1174621262810.2265997914780.1571853433140.000631662866288-0.04867475771160.3124383192940.004394178545530.36197231598827.059914604942.6048625214-12.3049658572
67.627494627735.37543615375-3.031725959165.58624278307-3.064272460372.961480300730.03380579853460.116425498390.52828325008-0.1343850340770.06103164729450.261002533008-0.0831913942239-0.213160495334-0.1678941355710.1092215163690.0421106602558-0.002506432122610.108391552875-0.002983448173150.1344605059169.9952800826242.0424679233-13.5935295415
74.181848194560.655136678388-2.060786882181.86595476715-0.2002450467312.95798144153-0.190017053387-0.289630210732-0.5163189742090.0660692532625-0.0775480113207-0.08424654213550.2645347007980.1331823698690.2246209115580.1110709620610.03969976146040.000941703744160.1568530499990.04036575633990.16348285643812.449883300130.6950140533-9.93107618449
85.098546957481.58908080357-2.373807712985.22781456041-2.669966976684.609101973320.0340325087318-0.5122903149070.1905159616650.432612822996-0.107706933208-0.589566982078-0.2944133068730.0270141271080.1227162278320.1368560897770.0278579088348-0.04114759406140.18761726969-0.02745031012720.16920292513616.309868229943.7977560655-6.55504182487
93.88455894127-0.9508937193910.5087864333870.2705708854340.1313246744842.05181179466-0.0104735836751-0.2717770562-0.5365372943590.2956837251290.018991554128-0.07374134026771.014712227760.264514555409-0.1583791814260.5155726095550.187813823873-0.07922305905210.2027129295020.03097375073130.28090732252314.83470646669.44751809276-38.4166664674
101.5263248364-1.23068576907-1.774885332744.742324430911.723240018752.06292313163-0.169542846841-0.4470009715420.02445539729360.6449304060150.492425977381-0.2582697663810.3941432742310.480833233137-0.03088996478420.7447182553030.408980527772-0.04109209621180.0380542979399-0.1337466434870.22044564645911.053561015512.1275289528-33.4546142864
111.34264068999-1.45482587719-1.255395020742.588908577921.262280581971.244945002310.1876649670340.160195215531-0.118687281466-0.657315227895-0.204653805242-0.06096418331240.2601073733130.351181059804-0.03988782803920.6426050670770.272872587144-0.03005173156720.284865274288-0.02824975747420.21697563809415.996599414510.8471667408-46.7720638076
120.08471353475960.120274865079-0.06238880083125.934970469513.60163166692.69031750522-0.0592009321830.04311944984030.189681757445-0.6410845589870.334588764295-0.9126310661180.697234667961.08011656068-0.2455772142940.3285031383760.1831535656050.02681194619230.26844286094-0.0553927393240.24279169901118.476039253223.4037526438-46.2036490489
131.7861364023-0.3847575156730.06518452191981.19567920332-0.3698669917130.961616455907-0.185457922816-0.0180415474778-0.1854224166890.1134125355950.226824761347-0.04955186054330.447520654320.276124882866-0.02192591406690.3296717852170.127365551698-0.03516014073680.167312632795-0.05201564385980.1561030314639.540490214918.5081446873-40.9276073487
142.37901217313-1.01170653866-1.462587578786.425175004664.817709981197.8381384002-0.1952378812270.264717438147-0.499617289297-0.224979588271-0.07187849266780.7380032984880.281086948428-0.1341053016710.2611851167150.288296779929-0.0892021478268-0.006949630261670.167398375127-0.02109781572940.352678309193-9.6309582652518.3824138988-46.0158970056
158.218074379643.9040007192-2.943260160283.48568839923-1.762052904952.949459974810.02163275495620.09623090009910.2048282712660.1257327445350.1067108872850.111744751543-0.2496276777-0.062880562772-0.2006375346690.1730729334170.0037784275675-0.04668731148890.0192791663079-0.004549642481510.110351998264-2.2657862259833.9925065389-45.0710408929
162.599101976690.451299137518-0.3476053325472.544258034890.05485061278142.19564803338-0.1525573284440.268283618054-0.194957484296-0.3500463959270.1207079940530.01561601418350.2117797881990.124375715368-0.01126285707820.256671854982-0.0321483056908-0.05298671407560.0677863504544-0.0349257814050.08671943529061.6812520443627.7290478065-49.9701416659
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 84 )
3X-RAY DIFFRACTION3chain 'A' and (resid 85 through 98 )
4X-RAY DIFFRACTION4chain 'A' and (resid 99 through 119 )
5X-RAY DIFFRACTION5chain 'A' and (resid 120 through 128 )
6X-RAY DIFFRACTION6chain 'A' and (resid 129 through 149 )
7X-RAY DIFFRACTION7chain 'A' and (resid 150 through 179 )
8X-RAY DIFFRACTION8chain 'A' and (resid 180 through 199 )
9X-RAY DIFFRACTION9chain 'B' and (resid 25 through 41 )
10X-RAY DIFFRACTION10chain 'B' and (resid 42 through 52 )
11X-RAY DIFFRACTION11chain 'B' and (resid 53 through 67 )
12X-RAY DIFFRACTION12chain 'B' and (resid 68 through 84 )
13X-RAY DIFFRACTION13chain 'B' and (resid 85 through 119 )
14X-RAY DIFFRACTION14chain 'B' and (resid 120 through 128 )
15X-RAY DIFFRACTION15chain 'B' and (resid 129 through 149 )
16X-RAY DIFFRACTION16chain 'B' and (resid 150 through 199 )

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