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- PDB-8ias: Crystal structure of Streptococcus pneumoniae pyruvate kinase -

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Basic information

Entry
Database: PDB / ID: 8ias
TitleCrystal structure of Streptococcus pneumoniae pyruvate kinase
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
CITRIC ACID / Pyruvate kinase
Similarity search - Component
Biological speciesStreptococcus pneumoniae R6 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)228,4517
Polymers227,9744
Non-polymers4763
Water15,439857
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11240 Å2
ΔGint-37 kcal/mol
Surface area74000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.094, 84.705, 107.012
Angle α, β, γ (deg.)101.22, 96.82, 91.42
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Pyruvate kinase


Mass: 56993.590 Da / Num. of mol.: 4
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-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H8O7
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 857 / 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: 2.9 Å3/Da / Density % sol: 57.65 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 50mM Sodium citrate pH5.5, 11% PEG1000, 10mM Na HEPES pH7.5, 75mM NaCl

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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 26, 2021
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→49.07 Å / Num. obs: 168397 / % possible obs: 96.7 % / Redundancy: 3.58 % / CC1/2: 0.997 / Rmerge(I) obs: 0.087 / Rrim(I) all: 0.102 / Net I/σ(I): 9.78
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique obsCC1/2Rrim(I) allDiffraction-ID
2-2.120.785270980.6920.9291
2.12-2.260.484256400.8430.5721
2.26-2.450.313239050.9440.3651
2.45-2.680.206221140.9670.2411
2.68-2.990.131198280.9820.1551
2.99-3.450.08173820.9910.0951
3.45-4.230.057148250.9940.0671
4.23-5.950.048112380.9950.0571
5.95-49.070.04263670.9980.0491

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Processing

Software
NameVersionClassification
REFMAC5refinement
XDSdata scaling
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→49.07 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.955 / Cross valid method: THROUGHOUT / ESU R: 0.151 / ESU R Free: 0.141 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21519 8420 5 %RANDOM
Rwork0.17809 ---
obs0.17996 159970 96.77 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 39.222 Å2
Baniso -1Baniso -2Baniso -3
1-0.75 Å2-0.34 Å20.29 Å2
2--1.56 Å2-0.93 Å2
3----1.79 Å2
Refinement stepCycle: 1 / Resolution: 2→49.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15344 0 32 857 16233
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.01315553
X-RAY DIFFRACTIONr_bond_other_d0.0360.01714996
X-RAY DIFFRACTIONr_angle_refined_deg1.4651.64320979
X-RAY DIFFRACTIONr_angle_other_deg2.3041.58334760
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.42751998
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.68123.05800
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.494152882
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.54715108
X-RAY DIFFRACTIONr_chiral_restr0.0730.22134
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0217490
X-RAY DIFFRACTIONr_gen_planes_other0.0080.023034
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_it3.183.868004
X-RAY DIFFRACTIONr_mcbond_other3.1753.8598003
X-RAY DIFFRACTIONr_mcangle_it4.2865.7689998
X-RAY DIFFRACTIONr_mcangle_other4.2865.7699999
X-RAY DIFFRACTIONr_scbond_it4.554.4977549
X-RAY DIFFRACTIONr_scbond_other4.5494.4977550
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.0026.4910982
X-RAY DIFFRACTIONr_long_range_B_refined8.7774.98565562
X-RAY DIFFRACTIONr_long_range_B_other8.76274.96465150
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.049 Å
RfactorNum. reflection% reflection
Rfree0.286 613 -
Rwork0.276 11637 -
obs--95.16 %

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