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- PDB-5nod: PASTA subunit 4 of Streptococcus pneumoniae STKP crystallized wit... -

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Basic information

Entry
Database: PDB / ID: 5nod
TitlePASTA subunit 4 of Streptococcus pneumoniae STKP crystallized with PEG and succinate
ComponentsSerine/threonine-protein kinase StkP
KeywordsTRANSFERASE / PASTA / extracellular domain / Ser/Thr kinase / Streptococcus pneumoniae
Function / homology
Function and homology information


protein serine/threonine kinase activity => GO:0004674 / division septum assembly / regulation of cell shape / membrane => GO:0016020 / non-specific serine/threonine protein kinase / protein serine kinase activity / protein serine/threonine kinase activity / ATP binding / plasma membrane
Similarity search - Function
PASTA domain / PASTA domain / PASTA domain profile. / PASTA / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. ...PASTA domain / PASTA domain / PASTA domain profile. / PASTA / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic 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
Serine/threonine-protein kinase StkP
Similarity search - Component
Biological speciesStreptococcus pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsGalisson, F. / Gueguen-Chaignon, V. / Gouet, P. / Grangeasse, C. / Zucchini, L.
CitationJournal: Nat Microbiol / Year: 2018
Title: PASTA repeats of the protein kinase StkP interconnect cell constriction and separation of Streptococcus pneumoniae.
Authors: Zucchini, L. / Mercy, C. / Garcia, P.S. / Cluzel, C. / Gueguen-Chaignon, V. / Galisson, F. / Freton, C. / Guiral, S. / Brochier-Armanet, C. / Gouet, P. / Grangeasse, C.
History
DepositionApr 12, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 8, 2017Provider: repository / Type: Initial release
Revision 1.1Dec 13, 2017Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 31, 2018Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.3Jun 12, 2019Group: Data collection / Structure summary
Category: audit_author / database_PDB_rev / database_PDB_rev_record
Item: _audit_author.name
Revision 1.4Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Serine/threonine-protein kinase StkP


Theoretical massNumber of molelcules
Total (without water)9,0841
Polymers9,0841
Non-polymers00
Water68538
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area4840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.760, 87.760, 40.958
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522

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Components

#1: Protein Serine/threonine-protein kinase StkP / Ser/Thr-protein kinase StkP / Eukaryotic-type Ser/Thr protein kinase / ESTPK


Mass: 9084.471 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pneumoniae (strain ATCC BAA-255 / R6) (bacteria)
Gene: stkP, pkn2, spr1577 / Production host: Escherichia coli (E. coli)
References: UniProt: Q8DNS0, non-specific serine/threonine protein kinase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 38 / 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: 2.51 Å3/Da / Density % sol: 50.92 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 15% PEG3350 0,1M Succinate pH 7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1.00003 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Oct 18, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00003 Å / Relative weight: 1
ReflectionResolution: 1.9→19.774 Å / Num. obs: 7718 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 12.386 % / Biso Wilson estimate: 29.75 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.042 / Rpim(I) all: 0.012 / Rrim(I) all: 0.041 / Rsym value: 0.042 / Χ2: 0.97 / Net I/av σ(I): 43.06 / Net I/σ(I): 42.7
Reflection shellResolution: 1.9→1.95 Å / Redundancy: 11.773 % / Rmerge(I) obs: 0.577 / Mean I/σ(I) obs: 4.67 / Num. unique obs: 550 / CC1/2: 0.943 / Rpim(I) all: 0.164 / Rrim(I) all: 0.603 / Rsym value: 0.577 / % possible all: 100

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Processing

Software
NameVersionClassification
XDSdata reduction
PHENIX1.11.1_2575refinement
PDB_EXTRACT3.22data extraction
MOLREPphasing
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3OUV

3ouv


Resolution: 1.9→19.774 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 27.75
RfactorNum. reflection% reflection
Rfree0.2245 464 6.01 %
Rwork0.2091 --
obs0.2101 7716 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 69.94 Å2 / Biso mean: 35.1098 Å2 / Biso min: 18.84 Å2
Refinement stepCycle: final / Resolution: 1.9→19.774 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms564 0 0 38 602
Biso mean---40.38 -
Num. residues----75
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008570
X-RAY DIFFRACTIONf_angle_d0.863771
X-RAY DIFFRACTIONf_chiral_restr0.05796
X-RAY DIFFRACTIONf_plane_restr0.00497
X-RAY DIFFRACTIONf_dihedral_angle_d2.364358
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 3 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.9001-2.17470.25021500.203423412491
2.1747-2.73870.27491530.227123902543
2.7387-19.77480.20331610.203925212682

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