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- PDB-7wcf: Crystal structure of the kinase with AMP-PNP -

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Basic information

Entry
Database: PDB / ID: 7wcf
TitleCrystal structure of the kinase with AMP-PNP
ComponentsHipA_C domain-containing protein
KeywordsTOXIN / A toxin wildspread in the prokaryote cells.
Function / homologyHipA-like, C-terminal / HipA-like C-terminal domain / transferase activity / PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER / HipA-like C-terminal domain-containing protein
Function and homology information
Biological speciesLegionella pneumophila subsp. pneumophila str. Philadelphia 1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.3636 Å
AuthorsOuyang, S.Y. / Zhen, X.
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
DepositionDec 20, 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 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: HipA_C domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,7154
Polymers37,1611
Non-polymers5543
Water6,864381
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area200 Å2
ΔGint-16 kcal/mol
Surface area15740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.989, 85.403, 92.557
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 / Lpg protein


Mass: 37160.777 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Legionella pneumophila subsp. pneumophila str. Philadelphia 1 (bacteria)
Strain: Philadelphia 1 / ATCC 33152 / DSM 7513 / Gene: lpg2370 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q5ZSZ6
#2: Chemical ChemComp-ACP / PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER / ADENOSINE-5'-[BETA, GAMMA-METHYLENE]TRIPHOSPHATE


Mass: 505.208 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H18N5O12P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: AMP-PCP, energy-carrying molecule analogue*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 381 / 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: 2.13 Å3/Da / Density % sol: 42.16 %
Crystal growTemperature: 289 K / Method: vapor diffusion / pH: 6.2 / Details: 10% Tacsimate pH 6.2, 20% PEG3350 / PH range: 6-9

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.9792 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 30, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.3636→62.77 Å / Num. obs: 64543 / % possible obs: 95 % / Redundancy: 7.4 % / CC1/2: 0.999 / Rmerge(I) obs: 0.049 / Net I/σ(I): 20.9
Reflection shellResolution: 1.364→1.44 Å / Num. unique obs: 7007 / CC1/2: 0.776

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
HKL-2000data scaling
MOLREPphasing
PHENIX1.11.1_2575refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7VKB

7vkb


Resolution: 1.3636→19.468 Å / SU ML: 0.13 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 21.55 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2 3166 4.91 %
Rwork0.1786 61283 -
obs0.1797 64449 94.24 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 59.42 Å2 / Biso mean: 23.9317 Å2 / Biso min: 12.13 Å2
Refinement stepCycle: final / Resolution: 1.3636→19.468 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2605 0 33 381 3019
Biso mean--16.71 32.6 -
Num. residues----319
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062688
X-RAY DIFFRACTIONf_angle_d0.9493622
X-RAY DIFFRACTIONf_chiral_restr0.075398
X-RAY DIFFRACTIONf_plane_restr0.005455
X-RAY DIFFRACTIONf_dihedral_angle_d7.8441028
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.3636-1.3840.3691870.281179163
1.384-1.40560.2353780.2501194169
1.4056-1.42860.25811040.2427216177
1.4286-1.45320.26911220.2366228883
1.4532-1.47970.27531220.2239256291
1.4797-1.50810.21331230.2214272798
1.5081-1.53890.21991510.20982826100
1.5389-1.57230.23121310.20522787100
1.5723-1.60890.23181480.19672795100
1.6089-1.64910.22121420.19362804100
1.6491-1.69370.21071470.19932793100
1.6937-1.74350.20341450.19342840100
1.7435-1.79970.23651330.19332802100
1.7997-1.8640.20851570.18872783100
1.864-1.93850.20521430.1802281799
1.9385-2.02670.21421210.1841280499
2.0267-2.13340.21291690.17772821100
2.1334-2.26690.17561500.1769279399
2.2669-2.44160.20131660.183281599
2.4416-2.68670.21461570.1797280699
2.6867-3.07420.18611740.1802281498
3.0742-3.86820.18411300.1603284197
3.8682-19.4680.17981660.1564287295

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