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- PDB-8xw6: Crystal structure of Streptococcus pneumoniae pyruvate kinase in ... -

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Basic information

Entry
Database: PDB / ID: 8xw6
TitleCrystal structure of Streptococcus pneumoniae pyruvate kinase in complex with oxalate and fructose 1,6-bisphosphate and ATP
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
ADENOSINE-5'-TRIPHOSPHATE / 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: 1.99 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)115,50212
Polymers113,9872
Non-polymers1,51510
Water9,170509
1
A: Pyruvate kinase
B: Pyruvate kinase
hetero molecules

A: Pyruvate kinase
B: Pyruvate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)231,00324
Polymers227,9744
Non-polymers3,02920
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_645y+1,x-1,-z+1/41
Buried area17660 Å2
ΔGint-113 kcal/mol
Surface area72460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.580, 81.580, 402.000
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
#6: 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, 517 molecules

#2: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#3: Chemical ChemComp-MG / MAGNESIUM ION


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


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


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 509 / 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: 2.93 Å3/Da / Density % sol: 58.08 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 10mM HEPES pH7.5, 75mM NaCl, 75mM KCl, 100mM Na Acetate, 16% PEG3350, 10mM Oxalate, 10mM FBP, 5mM ATP

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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: 1.99→46.96 Å / Num. obs: 93443 / % possible obs: 99.3 % / Redundancy: 8.1 % / CC1/2: 0.999 / Rmerge(I) obs: 0.078 / Rrim(I) all: 0.084 / Net I/σ(I): 13.59
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique obsCC1/2Rrim(I) allDiffraction-ID
1.99-2.121.057146630.7161.1281
2.12-2.260.564139770.8950.6021
2.26-2.440.342130110.9590.3631
2.44-2.670.222120850.9830.2361
2.67-2.990.143109760.9920.1531
2.99-3.450.08397850.9970.0891
3.45-4.220.05783650.9980.0611
4.22-5.940.04766260.9990.0511
5.94-46.960.03639550.9990.0381

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
XDSdata scaling
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.99→46.96 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.96 / Cross valid method: THROUGHOUT / ESU R: 0.14 / ESU R Free: 0.131 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21109 4661 5 %RANDOM
Rwork0.17835 ---
obs0.18001 88545 99.14 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 47.946 Å2
Baniso -1Baniso -2Baniso -3
1--0.85 Å20 Å20 Å2
2---0.85 Å20 Å2
3---1.7 Å2
Refinement stepCycle: 1 / Resolution: 1.99→46.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7680 0 88 509 8277
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0137853
X-RAY DIFFRACTIONr_bond_other_d0.0360.0177522
X-RAY DIFFRACTIONr_angle_refined_deg1.7141.65310608
X-RAY DIFFRACTIONr_angle_other_deg2.3521.58617443
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.59751000
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.11222.985402
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.365151444
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.5511554
X-RAY DIFFRACTIONr_chiral_restr0.0810.21082
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.028773
X-RAY DIFFRACTIONr_gen_planes_other0.0120.021520
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_it3.9914.7464006
X-RAY DIFFRACTIONr_mcbond_other3.9874.7454005
X-RAY DIFFRACTIONr_mcangle_it5.1447.1025004
X-RAY DIFFRACTIONr_mcangle_other5.1467.1035005
X-RAY DIFFRACTIONr_scbond_it5.6545.4453847
X-RAY DIFFRACTIONr_scbond_other5.6535.4463843
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other8.2727.885599
X-RAY DIFFRACTIONr_long_range_B_refined9.456.668455
X-RAY DIFFRACTIONr_long_range_B_other9.39956.6638456
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.995→2.047 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.327 331 -
Rwork0.32 6278 -
obs--97.01 %

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