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- PDB-5x1q: PpkA-294 with ATP and MnCl2 -

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Basic information

Entry
Database: PDB / ID: 5x1q
TitlePpkA-294 with ATP and MnCl2
ComponentsPpkA-294
KeywordsTRANSFERASE / ATP / kinase / Mg
Function / homology
Function and homology information


protein kinase activity / ATP binding
Similarity search - Function
Protein kinase domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / : / PpkA N terminal
Similarity search - Component
Biological speciesSerratia sp. FS14 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.602 Å
AuthorsLi, P.P. / Ran, T.T. / Xu, D.Q. / Wang, W.W.
Funding support China, 5items
OrganizationGrant numberCountry
Natural Science Foundation of China31400055 China
Natural Science Foundation of China31170686 China
Natural Science Foundation of China31100028 China
the Natural Science Foundation of Jiangsu ProvinceBK20140690 China
the Youth Science and Technology Innovation Fund from Nanjing Agricultural UniversityKJ2013027 China
CitationJournal: Biochem.J. / Year: 2018
Title: Crystal structures of the kinase domain of PpkA, a key regulatory component of T6SS, reveal a general inhibitory mechanism.
Authors: Li, P.P. / Xu, D.Q. / Ma, T.Q. / Wang, D.Y. / Li, W.D. / He, J.H. / Ran, T.T. / Wang, W.W.
History
DepositionJan 26, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 31, 2018Provider: repository / Type: Initial release
Revision 1.1Aug 21, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _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 1.2Mar 20, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PpkA-294
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,7664
Polymers34,1121
Non-polymers6543
Water4,648258
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area860 Å2
ΔGint-4 kcal/mol
Surface area12910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.898, 78.315, 59.188
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein PpkA-294


Mass: 34112.215 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Serratia sp. FS14 (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1S4NYE5*PLUS
#2: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE / Adenosine triphosphate


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#3: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 258 / Source method: isolated from a natural source / Formula: H2O

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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: 2.24 Å3/Da / Density % sol: 45.06 %
Crystal growTemperature: 295 K / Method: evaporation / pH: 7.5 / Details: PEG 400, Ammonium Sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97853 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: AREA DETECTOR / Date: Nov 9, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 1.6→20 Å / Num. obs: 40597 / % possible obs: 99 % / Observed criterion σ(I): 2 / Redundancy: 13 % / Rmerge(I) obs: 0.05 / Rpim(I) all: 0.014 / Net I/σ(I): 29.5
Reflection shellResolution: 1.6→1.69 Å / Redundancy: 12 % / Rmerge(I) obs: 0.333 / Num. unique obs: 5502 / Rpim(I) all: 0.098 / % possible all: 93.5

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Processing

Software
NameVersionClassification
PHENIX(dev_2247: ???)refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementResolution: 1.602→19.916 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 20.47
RfactorNum. reflection% reflection
Rfree0.2123 2009 4.95 %
Rwork0.1793 --
obs0.1809 40551 98.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.602→19.916 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2251 0 38 258 2547
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072346
X-RAY DIFFRACTIONf_angle_d1.053190
X-RAY DIFFRACTIONf_dihedral_angle_d16.5861404
X-RAY DIFFRACTIONf_chiral_restr0.055345
X-RAY DIFFRACTIONf_plane_restr0.006416
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6017-1.64180.2411220.19892370X-RAY DIFFRACTION86
1.6418-1.68610.22811490.18262711X-RAY DIFFRACTION100
1.6861-1.73570.21481400.18642766X-RAY DIFFRACTION100
1.7357-1.79170.21361590.18052715X-RAY DIFFRACTION100
1.7917-1.85570.21841580.18552727X-RAY DIFFRACTION100
1.8557-1.92990.23091450.1842757X-RAY DIFFRACTION100
1.9299-2.01770.22151310.17662765X-RAY DIFFRACTION100
2.0177-2.1240.19331430.18552770X-RAY DIFFRACTION100
2.124-2.25690.19591240.18332787X-RAY DIFFRACTION100
2.2569-2.43080.2321230.1852787X-RAY DIFFRACTION100
2.4308-2.67490.22291520.19042786X-RAY DIFFRACTION100
2.6749-3.06080.24331460.19232802X-RAY DIFFRACTION100
3.0608-3.85170.22171430.17292850X-RAY DIFFRACTION100
3.8517-19.9180.17961740.16232949X-RAY DIFFRACTION100

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