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- PDB-7vkb: Crystal structure of the a bacterial kinase complex -

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Basic information

Entry
Database: PDB / ID: 7vkb
TitleCrystal structure of the a bacterial kinase complex
Components
  • HipA (Persistence to inhibition of murein or DNA biosynthesis)
  • HipA_C domain-containing protein
KeywordsTOXIN/ANTITOXIN / TOXIN ANTITOXIN SYSTEM / TOXIN / TOXIN-ANTITOXIN complex
Function / homology
Function and homology information


protein serine/threonine kinase activity / metal ion binding / cytosol
Similarity search - Function
: / HipA, N-terminal subdomain 1 / HipA N-terminal domain / HipA-like, C-terminal / HipA-like C-terminal domain
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / HipA-like C-terminal domain-containing protein / HipA (Persistence to inhibition of murein or DNA biosynthesis)
Similarity search - Component
Biological speciesLegionella pneumophila subsp. pneumophila str. Philadelphia 1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.82 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
Revision 1.2Oct 23, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HipA_C domain-containing protein
B: HipA (Persistence to inhibition of murein or DNA biosynthesis)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,7964
Polymers48,6672
Non-polymers1292
Water4,378243
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2440 Å2
ΔGint-13 kcal/mol
Surface area17620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.220, 45.220, 394.550
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-529-

HOH

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Components

#1: Protein HipA_C domain-containing protein


Mass: 36957.707 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-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q5ZSZ6
#2: Protein HipA (Persistence to inhibition of murein or DNA biosynthesis)


Mass: 11709.013 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: lpg2369 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q5ZSZ7
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 243 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.07 Å3/Da / Density % sol: 40.64 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7.2 / Details: 0.1M Sodium acetate PH 7.0 12% 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: 0.97981 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 30, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97981 Å / Relative weight: 1
ReflectionResolution: 1.82→31.871 Å / Num. obs: 38842 / % possible obs: 100 % / Redundancy: 15.1 % / Biso Wilson estimate: 38.79 Å2 / CC1/2: 1 / Net I/σ(I): 2
Reflection shellResolution: 1.82→1.87 Å / Rmerge(I) obs: 0.089 / Num. unique obs: 2774 / CC1/2: 0.801 / Rpim(I) all: 0.091 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
HKL-2000data scaling
PDB_EXTRACT3.27data extraction
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 1.82→31.87 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 23.51 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.246 1894 4.9 %
Rwork0.2047 36766 -
obs0.2068 38660 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 160.45 Å2 / Biso mean: 46.2556 Å2 / Biso min: 27.28 Å2
Refinement stepCycle: final / Resolution: 1.82→31.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2924 0 8 243 3175
Biso mean--62.32 49.3 -
Num. residues----363
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.82-1.870.32511200.269225472667
1.87-1.920.33021220.248725642686
1.92-1.970.29651480.229825642712
1.97-2.040.27871340.226425432677
2.04-2.110.24071070.226425972704
2.11-2.190.21271480.203125662714
2.19-2.290.22951290.208725972726
2.29-2.410.25521460.210925652711
2.41-2.560.24271190.214726262745
2.56-2.760.28911440.224626092753
2.76-3.040.26491390.215126562795
3.04-3.480.23991290.208427002829
3.48-4.380.211420.173226902832
4.38-31.870.25411670.206929423109
Refinement TLS params.Method: refined / Origin x: 25.8055 Å / Origin y: 18.4674 Å / Origin z: 73.6968 Å
111213212223313233
T0.1351 Å20.0188 Å20.0224 Å2-0.2203 Å2-0.0262 Å2--0.223 Å2
L1.1208 °20.3686 °20.5591 °2-0.665 °2-0.0297 °2--2.1078 °2
S0.0754 Å °-0.0319 Å °0.1227 Å °0.0891 Å °-0.0836 Å °0.0081 Å °0.1117 Å °-0.1821 Å °-0.0032 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA52 - 312
2X-RAY DIFFRACTION1allB1 - 102
3X-RAY DIFFRACTION1allC1
4X-RAY DIFFRACTION1allD1
5X-RAY DIFFRACTION1allS1 - 243

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