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

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Basic information

Entry
Database: PDB / ID: 8iat
TitleCrystal structure of Streptococcus pneumoniae pyruvate kinase in complex with oxalate
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
: / OXALATE ION / TRIETHYLENE GLYCOL / 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)229,51924
Polymers227,9744
Non-polymers1,54420
Water18,3571019
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12040 Å2
ΔGint-53 kcal/mol
Surface area74690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)212.051, 118.353, 99.820
Angle α, β, γ (deg.)90.00, 108.93, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-945-

HOH

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Components

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Protein , 1 types, 4 molecules ABCD

#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

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Non-polymers , 7 types, 1039 molecules

#2: Chemical
ChemComp-OXL / OXALATE ION


Mass: 88.019 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2O4
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: K
#5: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#6: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O4
#7: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 1019 / 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: 2.6 Å3/Da / Density % sol: 52.67 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 1% Tacsimate pH 6.0, 50mM BIS-TRIS pH 6.5, 10%PEG3350, 10mM Na HEPES HCl pH7.5, 75mM NaCl, 10mM MgCl2, 50mM KCl, 10mM Oxalate

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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: Feb 5, 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: 1.8→48.3 Å / Num. obs: 215295 / % possible obs: 99.7 % / Redundancy: 6.96 % / CC1/2: 0.996 / Rmerge(I) obs: 0.09 / Rrim(I) all: 0.097 / Net I/σ(I): 10.84
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique obsCC1/2Rrim(I) allDiffraction-ID
1.8-1.910.869344490.8730.9391
1.91-2.040.481326740.9480.5211
2.04-2.20.278304160.980.2991
2.2-2.410.167280250.9890.1811
2.41-2.690.124253870.990.1341
2.69-3.110.096223800.9930.1041
3.11-3.810.078189730.9940.0841
3.81-5.360.072147120.9940.0781
5.36-48.30.0782790.9960.0751

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Processing

Software
NameVersionClassification
REFMAC5refinement
XDSdata scaling
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→48.3 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.951 / Cross valid method: THROUGHOUT / ESU R: 0.125 / ESU R Free: 0.128 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24584 10764 5 %RANDOM
Rwork0.19865 ---
obs0.20103 204517 99.74 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 44.738 Å2
Baniso -1Baniso -2Baniso -3
1--2 Å20 Å20.77 Å2
2--0.97 Å2-0 Å2
3---0.4 Å2
Refinement stepCycle: 1 / Resolution: 1.8→48.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15347 0 95 1019 16461
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.01315628
X-RAY DIFFRACTIONr_bond_other_d0.0360.01715054
X-RAY DIFFRACTIONr_angle_refined_deg1.5561.64321060
X-RAY DIFFRACTIONr_angle_other_deg2.3341.58234899
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.47252003
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.86722.946808
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.853152887
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.79415107
X-RAY DIFFRACTIONr_chiral_restr0.0720.22137
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0217557
X-RAY DIFFRACTIONr_gen_planes_other0.010.023044
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_it3.7794.5338018
X-RAY DIFFRACTIONr_mcbond_other3.7794.5338017
X-RAY DIFFRACTIONr_mcangle_it4.9576.78310019
X-RAY DIFFRACTIONr_mcangle_other4.9576.78310020
X-RAY DIFFRACTIONr_scbond_it4.3915.0177609
X-RAY DIFFRACTIONr_scbond_other4.3915.0177610
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.4157.32311042
X-RAY DIFFRACTIONr_long_range_B_refined9.56554.51617288
X-RAY DIFFRACTIONr_long_range_B_other9.31754.33117113
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.845 Å
RfactorNum. reflection% reflection
Rfree0.421 779 -
Rwork0.379 14812 -
obs--98.03 %

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