[English] 日本語
Yorodumi
- PDB-6pwd: Ewingella americana HopBF1 kinase -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6pwd
TitleEwingella americana HopBF1 kinase
ComponentsType III effector HopBF1
KeywordsTRANSFERASE / HSP90 / phosphorylation / chaperone / immunity / kinase
Function / homology: / Transferases; Transferring phosphorus-containing groups; Phosphotransferases with an alcohol group as acceptor / kinase activity / host cell / extracellular region / ATP binding / Type III effector protein 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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


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


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


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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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 )

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more