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- PDB-8xw7: Crystal structure of Streptococcus pneumoniae pyruvate kinase in ... -

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Basic information

Entry
Database: PDB / ID: 8xw7
TitleCrystal structure of Streptococcus pneumoniae pyruvate kinase in complex with oxalate and fructose 1,6-bisphosphate and ADP
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
ADENOSINE-5'-DIPHOSPHATE / 1,6-di-O-phosphono-beta-D-fructofuranose / : / OXALATE ION / Pyruvate kinase
Similarity search - Component
Biological speciesStreptococcus pneumoniae R6 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsNakashima, R. / Taguchi, A.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS) Japan
CitationJournal: J.Mol.Biol. / Year: 2024
Title: Structural Basis of Nucleotide Selectivity in Pyruvate Kinase.
Authors: Taguchi, A. / Nakashima, R. / Nishino, K.
History
DepositionJan 16, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 31, 2024Provider: repository / Type: Initial release
Revision 1.1Aug 7, 2024Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Pyruvate kinase
B: Pyruvate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,96515
Polymers113,9872
Non-polymers1,97813
Water6,557364
1
A: Pyruvate kinase
B: Pyruvate kinase
hetero molecules

A: Pyruvate kinase
B: Pyruvate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)231,93130
Polymers227,9744
Non-polymers3,95626
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_554-x,y,-z-1/21
Buried area19720 Å2
ΔGint-161 kcal/mol
Surface area71280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)123.184, 255.539, 88.133
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11B-835-

HOH

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Components

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Protein / Sugars , 2 types, 4 molecules AB

#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
#4: 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.: 2 / Source method: obtained synthetically / Formula: C6H14O12P2
IdentifierTypeProgram
b-D-Fruf1PO36PO3IUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0

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Non-polymers , 6 types, 375 molecules

#2: Chemical
ChemComp-MG / MAGNESIUM ION


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


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#5: Chemical ChemComp-OXL / OXALATE ION


Mass: 88.019 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2O4
#6: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#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.: 364 / 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: 3.04 Å3/Da / Density % sol: 59.57 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 10mM HEPES pH7.5, 250mM NaCl, 75mM KCl, 20% PEG1000, 5% glycerol, 50mM tricine pH8.0, 10mM Oxalate, 10mM FBP, 5mM ADP

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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: Oct 12, 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: 2.1→47.22 Å / Num. obs: 81724 / % possible obs: 100 % / Redundancy: 9.2 % / CC1/2: 1 / Rmerge(I) obs: 0.067 / Rrim(I) all: 0.071 / Net I/σ(I): 19.63
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique obsCC1/2Rrim(I) allDiffraction-ID
2.1-2.220.938130440.8950.9981
2.22-2.380.55123030.9680.5821
2.38-2.570.345114750.9840.3661
2.57-2.810.191105550.9940.2031
2.81-3.140.1196270.9970.1181
3.14-3.620.05985040.9990.0631
3.62-4.430.03872430.9990.041
4.43-6.240.03356680.9990.0351
6.24-47.220.026330510.0281

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
XDSdata scaling
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→47.21 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.952 / Cross valid method: THROUGHOUT / ESU R: 0.169 / ESU R Free: 0.157 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22684 4086 5 %RANDOM
Rwork0.18615 ---
obs0.18815 77629 99.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 53.046 Å2
Baniso -1Baniso -2Baniso -3
1--3.85 Å2-0 Å20 Å2
2---2.09 Å2-0 Å2
3---5.94 Å2
Refinement stepCycle: 1 / Resolution: 2.1→47.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7672 0 118 364 8154
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0137875
X-RAY DIFFRACTIONr_bond_other_d0.0360.0177527
X-RAY DIFFRACTIONr_angle_refined_deg1.6571.65310641
X-RAY DIFFRACTIONr_angle_other_deg2.3451.58617457
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9165999
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.47922.985402
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.4151441
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.21554
X-RAY DIFFRACTIONr_chiral_restr0.0730.21085
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.028783
X-RAY DIFFRACTIONr_gen_planes_other0.010.021521
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_it4.5335.3884002
X-RAY DIFFRACTIONr_mcbond_other4.525.3874001
X-RAY DIFFRACTIONr_mcangle_it6.228.0724999
X-RAY DIFFRACTIONr_mcangle_other6.2198.0735000
X-RAY DIFFRACTIONr_scbond_it5.5056.0013873
X-RAY DIFFRACTIONr_scbond_other5.5046.0013874
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other8.1118.7575643
X-RAY DIFFRACTIONr_long_range_B_refined9.80464.9728584
X-RAY DIFFRACTIONr_long_range_B_other9.80364.9748585
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.1→2.151 Å
RfactorNum. reflection% reflection
Rfree0.414 299 -
Rwork0.419 5676 -
obs--99.75 %

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