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

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Basic information

Entry
Database: PDB / ID: 8iaw
TitleCrystal structure of Streptococcus pneumoniae pyruvate kinase in complex with phosphoenolpyruvate
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 / cytosol / cytoplasm
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
PHOSPHOENOLPYRUVATE / Pyruvate kinase
Similarity search - Component
Biological speciesStreptococcus pneumoniae R6 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.89 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,94812
Polymers113,9872
Non-polymers96110
Water37821
1
A: Pyruvate kinase
B: Pyruvate kinase
hetero molecules

A: Pyruvate kinase
B: Pyruvate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)229,89724
Polymers227,9744
Non-polymers1,92220
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation1
Buried area15300 Å2
ΔGint-296 kcal/mol
Surface area75140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.057, 110.372, 130.931
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 Pyruvate kinase


Mass: 56993.590 Da / Num. of mol.: 2
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: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-PEP / PHOSPHOENOLPYRUVATE


Mass: 168.042 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H5O6P
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 21 / Source method: isolated from a natural source / Formula: H2O
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: 3.04 Å3/Da / Density % sol: 59.6 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: Details about the temperature: 20mM MgCl2, 1mM CoCl2, 35mM Na HEPES-HCl pH7.5, 1M (NH4)2SO4, 0.5mM Spermine, 37.5mM NaCl,500mM KCl, 5mM PEP

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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: Nov 12, 2022
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: 2.89→50 Å / Num. obs: 31733 / % possible obs: 99.8 % / Redundancy: 5.56 % / CC1/2: 0.995 / Rmerge(I) obs: 0.171 / Rrim(I) all: 0.189 / Net I/σ(I): 9.68
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique obsCC1/2Rrim(I) allDiffraction-ID
2.89-3.071.0150450.8441.1191
3.07-3.280.60147120.910.6721
3.28-3.540.33744440.9750.3751
3.54-3.880.19740880.9910.2171
3.88-4.330.11937170.9960.1311
4.33-4.990.08233180.9970.0911
4.99-6.10.0928370.9960.11
6.1-8.560.05622410.9990.0621
8.56-500.03613310.9990.041

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
XDSdata scaling
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.89→48.58 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.91 / Cross valid method: THROUGHOUT / ESU R Free: 0.408 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27276 1586 5 %RANDOM
Rwork0.24082 ---
obs0.24244 30120 99.72 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 49.756 Å2
Baniso -1Baniso -2Baniso -3
1-2.19 Å20 Å20 Å2
2--4.37 Å2-0 Å2
3----6.56 Å2
Refinement stepCycle: 1 / Resolution: 2.89→48.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7680 0 52 21 7753
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0137812
X-RAY DIFFRACTIONr_bond_other_d0.0360.0177504
X-RAY DIFFRACTIONr_angle_refined_deg1.4771.64510542
X-RAY DIFFRACTIONr_angle_other_deg2.3421.58317390
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.18151000
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.99722.985402
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.511151444
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.1261554
X-RAY DIFFRACTIONr_chiral_restr0.0590.21068
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.028760
X-RAY DIFFRACTIONr_gen_planes_other0.0060.021522
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_it3.4255.1194006
X-RAY DIFFRACTIONr_mcbond_other3.4245.1184005
X-RAY DIFFRACTIONr_mcangle_it5.457.6725004
X-RAY DIFFRACTIONr_mcangle_other5.457.6735005
X-RAY DIFFRACTIONr_scbond_it3.8115.6443804
X-RAY DIFFRACTIONr_scbond_other3.7995.6443777
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.2948.2685501
X-RAY DIFFRACTIONr_long_range_B_refined10.61497.9731626
X-RAY DIFFRACTIONr_long_range_B_other10.61397.96831612
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 14984 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.11 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.892→2.967 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.333 114 -
Rwork0.365 2169 -
obs--99.43 %

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