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- PDB-8iax: Crystal structure of Streptococcus pneumoniae pyruvate kinase in ... -

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Basic information

Entry
Database: PDB / ID: 8iax
TitleCrystal structure of Streptococcus pneumoniae pyruvate kinase in complex with phosphoenolpyruvate and fructose 1,6-bisphosphate
ComponentsPyruvate kinase
KeywordsTRANSFERASE / Pyruvate kinase / Streptococcus pneumoniae / Glycolysis
Function / homology
Function and homology information


pyruvate kinase / pyruvate kinase activity / potassium ion binding / glycolytic process / kinase activity / magnesium ion binding / ATP binding / cytoplasm / cytosol
Similarity search - Function
Pyruvate kinase / Pyruvate kinase, barrel / Pyruvate kinase, insert domain superfamily / Pyruvate kinase, barrel domain / Pyruvate kinase, C-terminal / Pyruvate kinase, C-terminal domain superfamily / Pyruvate kinase, alpha/beta domain / Pyruvate kinase-like, insert domain superfamily / Pyruvate kinase-like domain superfamily / Pyruvate/Phosphoenolpyruvate kinase-like domain superfamily
Similarity search - Domain/homology
1,6-di-O-phosphono-beta-D-fructofuranose / : / PHOSPHOENOLPYRUVATE / Pyruvate kinase
Similarity search - Component
Biological speciesStreptococcus pneumoniae R6 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsNakashima, R. / Taguchi, A.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)21K20759 Japan
CitationJournal: J.Biol.Chem. / Year: 2023
Title: Functional and structural characterization of Streptococcus pneumoniae pyruvate kinase involved in fosfomycin resistance.
Authors: Taguchi, A. / Nakashima, R. / Nishino, K.
History
DepositionFeb 9, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 14, 2023Provider: repository / Type: Initial release
Revision 1.1Jun 21, 2023Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation_author.identifier_ORCID
Revision 1.2Jul 19, 2023Group: Data collection / Database references / Category: citation / diffrn_source
Item: _citation.journal_volume / _diffrn_source.pdbx_synchrotron_site
Revision 1.3May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond / diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Pyruvate kinase
B: Pyruvate kinase
C: Pyruvate kinase
D: Pyruvate kinase
E: Pyruvate kinase
F: Pyruvate kinase
G: Pyruvate kinase
H: Pyruvate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)460,52140
Polymers455,9498
Non-polymers4,57232
Water48,4422689
1
A: Pyruvate kinase
B: Pyruvate kinase
C: Pyruvate kinase
D: Pyruvate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)230,26120
Polymers227,9744
Non-polymers2,28616
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15810 Å2
ΔGint-127 kcal/mol
Surface area73860 Å2
MethodPISA
2
E: Pyruvate kinase
F: Pyruvate kinase
G: Pyruvate kinase
H: Pyruvate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)230,26120
Polymers227,9744
Non-polymers2,28616
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15780 Å2
ΔGint-125 kcal/mol
Surface area73900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)221.061, 86.644, 258.148
Angle α, β, γ (deg.)90.00, 100.86, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein / Sugars , 2 types, 16 molecules ABCDEFGH

#1: Protein
Pyruvate kinase


Mass: 56993.590 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pneumoniae R6 (bacteria) / Gene: pykF / Production host: Escherichia coli (E. coli) / References: UniProt: Q8DQ84
#2: Sugar
ChemComp-FBP / 1,6-di-O-phosphono-beta-D-fructofuranose / BETA-FRUCTOSE-1,6-DIPHOSPHATE / FRUCTOSE-1,6-BISPHOSPHATE / 1,6-di-O-phosphono-beta-D-fructose / 1,6-di-O-phosphono-D-fructose / 1,6-di-O-phosphono-fructose


Type: D-saccharide, beta linking / Mass: 340.116 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C6H14O12P2
IdentifierTypeProgram
b-D-Fruf1PO36PO3IUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0

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Non-polymers , 4 types, 2713 molecules

#3: Chemical
ChemComp-PEP / PHOSPHOENOLPYRUVATE


Mass: 168.042 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C3H5O6P
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mg
#5: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: K
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2689 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 2.66 Å3/Da / Density % sol: 53.8 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.75
Details: 8%(w/v) PEG3350, 50mM Citric acid/Bis-Tris Propan(3.75:6.25) pH6.75, 10mM Na HEPES HCl pH7.5, 75mM NaCl, 10mM MgCl2, 50mM KCl, 5mM PEP, 10mM FBP

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jan 21, 2023
Details: Main beamline optics is a double-crystal monochromator and a horizontal focusing mirror.
RadiationMonochromator: Double-crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.8→48.37 Å / Num. obs: 442679 / % possible obs: 99.6 % / Redundancy: 6.99 % / CC1/2: 0.999 / Rmerge(I) obs: 0.063 / Rrim(I) all: 0.068 / Net I/σ(I): 14.83
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique obsCC1/2Rrim(I) allDiffraction-ID
1.8-1.911.029705500.8011.111
1.91-2.040.546669350.9310.5911
2.04-2.20.292624830.9810.3151
2.2-2.410.164576490.9940.1771
2.41-2.690.102522270.9970.111
2.69-3.110.066460740.9980.0711
3.11-3.80.046391340.9990.051
3.8-5.360.039304430.9990.0421
5.36-48.370.034171840.9990.0371

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Processing

Software
NameVersionClassification
REFMAC5refinement
XDSdata scaling
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→48.37 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.962 / Cross valid method: THROUGHOUT / ESU R: 0.115 / ESU R Free: 0.115 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22121 22134 5 %RANDOM
Rwork0.18253 ---
obs0.18448 420531 99.59 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 39.959 Å2
Baniso -1Baniso -2Baniso -3
1--0.89 Å2-0 Å20.75 Å2
2---0.55 Å2-0 Å2
3---1.08 Å2
Refinement stepCycle: 1 / Resolution: 1.8→48.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms30720 0 256 2689 33665
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.01331312
X-RAY DIFFRACTIONr_bond_other_d0.0360.01730072
X-RAY DIFFRACTIONr_angle_refined_deg1.7621.65442280
X-RAY DIFFRACTIONr_angle_other_deg2.3561.58669712
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.74854000
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.98222.9851608
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.851155776
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.68115216
X-RAY DIFFRACTIONr_chiral_restr0.0840.24304
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0235040
X-RAY DIFFRACTIONr_gen_planes_other0.0140.026088
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.4853.94816024
X-RAY DIFFRACTIONr_mcbond_other3.4843.94816023
X-RAY DIFFRACTIONr_mcangle_it4.4015.90720016
X-RAY DIFFRACTIONr_mcangle_other4.4015.90720017
X-RAY DIFFRACTIONr_scbond_it4.7584.50415288
X-RAY DIFFRACTIONr_scbond_other4.7594.50415285
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.916.5222265
X-RAY DIFFRACTIONr_long_range_B_refined8.6647.77234583
X-RAY DIFFRACTIONr_long_range_B_other8.52347.42134041
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.844 Å
RfactorNum. reflection% reflection
Rfree0.413 1600 -
Rwork0.397 30402 -
obs--97.82 %

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