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- PDB-7vkc: Crystal structure of a bacterial Ser/Thr kinase -

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Basic information

Entry
Database: PDB / ID: 7vkc
TitleCrystal structure of a bacterial Ser/Thr kinase
ComponentsHipA_C domain-containing protein
KeywordsTOXIN / kinase / toxin antitoxin
Function / homologyHipA-like, C-terminal / HipA-like C-terminal domain / transferase activity / HipA-like C-terminal domain-containing protein
Function and homology information
Biological speciesLegionella pneumophila subsp. pneumophila str. Philadelphia 1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.46 Å
AuthorsZhen, X. / Ouyang, S.Y.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32170045 China
CitationJournal: Nat Commun / Year: 2022
Title: Molecular mechanism of toxin neutralization in the HipBST toxin-antitoxin system of Legionella pneumophila.
Authors: Zhen, X. / Wu, Y. / Ge, J. / Fu, J. / Ye, L. / Lin, N. / Huang, Z. / Liu, Z. / Luo, Z.Q. / Qiu, J. / Ouyang, S.
History
DepositionSep 29, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 29, 2022Provider: repository / Type: Initial release
Revision 1.1Aug 3, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: HipA_C domain-containing protein


Theoretical massNumber of molelcules
Total (without water)37,0381
Polymers37,0381
Non-polymers00
Water8,341463
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)52.948, 64.638, 90.416
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein HipA_C domain-containing protein


Mass: 37037.684 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Legionella pneumophila subsp. pneumophila str. Philadelphia 1 (bacteria)
Gene: lpg2370 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q5ZSZ6
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 463 / 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: 2.11 Å3/Da / Density % sol: 41.69 % / Description: cubic
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 8% Tacsimate PH 6.0, 20% PEG 3350 / PH range: 6-8

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9791 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 29, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 1.457→32.32 Å / Num. obs: 50396 / % possible obs: 100 % / Redundancy: 12.3 % / Biso Wilson estimate: 13.46 Å2 / CC1/2: 0.998 / Net I/σ(I): 2.2
Reflection shellResolution: 1.457→1.51 Å / Rmerge(I) obs: 0.1 / Num. unique obs: 1966 / CC1/2: 0.887

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
HKL-2000data scaling
PDB_EXTRACT3.27data extraction
HKL-3000data reduction
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 1.46→32.32 Å / SU ML: 0.12 / Cross valid method: THROUGHOUT / σ(F): 0.16 / Phase error: 20.21 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1848 1957 3.9 %
Rwork0.1671 48216 -
obs0.1678 50173 91.33 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 58.14 Å2 / Biso mean: 20.6968 Å2 / Biso min: 8.07 Å2
Refinement stepCycle: final / Resolution: 1.46→32.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2576 0 0 463 3039
Biso mean---31.92 -
Num. residues----316
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.46-1.490.2648820.23472016209854
1.49-1.530.249970.21882445254266
1.53-1.580.21771180.20562908302678
1.58-1.630.21051360.18723380351691
1.63-1.690.20641490.17683625377497
1.69-1.760.18361500.17163622377297
1.76-1.840.21191500.17223681383198
1.84-1.930.20381510.16713700385199
1.93-2.050.19721510.1593722387399
2.05-2.210.16651510.15863746389799
2.21-2.430.18721520.1623752390499
2.43-2.790.1721540.165938033957100
2.79-3.510.15971550.159938343989100
3.51-32.320.18351610.16253982414399
Refinement TLS params.Method: refined / Origin x: -35.4806 Å / Origin y: 68.1214 Å / Origin z: 101.2394 Å
111213212223313233
T0.1068 Å2-0.0172 Å2-0.0085 Å2-0.099 Å20.0138 Å2--0.1046 Å2
L0.4636 °2-0.1708 °20.055 °2-0.16 °2-0.0592 °2--0.3083 °2
S0.0077 Å °-0.0381 Å °-0.0247 Å °0.0025 Å °0.0129 Å °0.0046 Å °0.0258 Å °-0.0303 Å °0 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA-4 - 311
2X-RAY DIFFRACTION1allS1 - 463

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