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- PDB-8xw9: Crystal structure of Streptococcus pneumoniae pyruvate kinase in ... -

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Basic information

Entry
Database: PDB / ID: 8xw9
TitleCrystal structure of Streptococcus pneumoniae pyruvate kinase in complex with oxalate and fructose 1,6-bisphosphate and UDP
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 / : / OXALATE ION / URIDINE-5'-DIPHOSPHATE / Pyruvate kinase
Similarity search - Component
Biological speciesStreptococcus pneumoniae R6 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsNakashima, R. / Taguchi, A.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)21K20759 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)115,39912
Polymers113,9872
Non-polymers1,41210
Water16,412911
1
A: Pyruvate kinase
B: Pyruvate kinase
hetero molecules

A: Pyruvate kinase
B: Pyruvate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)230,79724
Polymers227,9744
Non-polymers2,82320
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z+1/41
Buried area17300 Å2
ΔGint-129 kcal/mol
Surface area73120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.464, 81.464, 398.910
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number95
Space group name H-MP4322

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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
#5: 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 , 5 types, 919 molecules

#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / 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
#4: Chemical ChemComp-OXL / OXALATE ION


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


Type: RNA linking / Mass: 404.161 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H14N2O12P2 / Comment: UDP*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 911 / 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: 2.9 Å3/Da / Density % sol: 57.63 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 10mM HEPES pH7.5, 75mM NaCl, 125mM KCl, 10mM Tris-HCl pH7.0, 14% PEG4000, 10mM Oxalate, 10mM FBP, 5mM UDP

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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: Dec 4, 2023
RadiationMonochromator: Double-crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.75→40.74 Å / Num. obs: 136776 / % possible obs: 99.5 % / Redundancy: 6 % / CC1/2: 0.999 / Rmerge(I) obs: 0.057 / Rrim(I) all: 0.063 / Net I/σ(I): 16.01
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique obsCC1/2Rrim(I) allDiffraction-ID
1.75-1.850.936216650.6721.0241
1.85-1.980.508204380.8910.5531
1.98-2.140.277191530.9640.3021
2.14-2.340.156176650.9880.1711
2.34-2.620.103160760.9930.1131
2.62-3.020.068143070.9970.0741
3.02-3.70.043121880.9980.0471
3.7-5.210.03295970.9990.0361
5.21-40.740.02456870.9990.0271

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
XDSdata scaling
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.75→40.73 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.966 / Cross valid method: THROUGHOUT / ESU R: 0.086 / ESU R Free: 0.088 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19057 6839 5 %RANDOM
Rwork0.16023 ---
obs0.16174 129937 99.48 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 34.335 Å2
Baniso -1Baniso -2Baniso -3
1-0.43 Å2-0 Å20 Å2
2--0.43 Å20 Å2
3----0.86 Å2
Refinement stepCycle: 1 / Resolution: 1.75→40.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7680 0 82 911 8673
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0137846
X-RAY DIFFRACTIONr_bond_other_d0.0360.0177523
X-RAY DIFFRACTIONr_angle_refined_deg1.7831.65710596
X-RAY DIFFRACTIONr_angle_other_deg2.3511.58817445
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.28651000
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.17822.985402
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.53151444
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.1231554
X-RAY DIFFRACTIONr_chiral_restr0.0910.21080
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.028765
X-RAY DIFFRACTIONr_gen_planes_other0.0170.021521
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_it2.953.2544006
X-RAY DIFFRACTIONr_mcbond_other2.9423.2534005
X-RAY DIFFRACTIONr_mcangle_it3.8324.8685004
X-RAY DIFFRACTIONr_mcangle_other3.8354.8695005
X-RAY DIFFRACTIONr_scbond_it4.9863.8753838
X-RAY DIFFRACTIONr_scbond_other4.9873.8753837
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.5615.5555593
X-RAY DIFFRACTIONr_long_range_B_refined8.5540.2538726
X-RAY DIFFRACTIONr_long_range_B_other8.5540.2468726
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.75→1.792 Å
RfactorNum. reflection% reflection
Rfree0.322 494 -
Rwork0.314 9384 -
obs--98.93 %

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