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

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Basic information

Entry
Database: PDB / ID: 8zly
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: 1.89 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
DepositionMay 21, 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

Downloads & links

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Assembly

Deposited unit
A: Pyruvate kinase
B: Pyruvate kinase
C: Pyruvate kinase
D: Pyruvate kinase
E: Pyruvate kinase
F: Pyruvate kinase
G: Pyruvate kinase
H: Pyruvate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)462,88054
Polymers455,9498
Non-polymers6,93246
Water69,3403849
1
A: Pyruvate kinase
B: Pyruvate kinase
hetero molecules

A: Pyruvate kinase
B: Pyruvate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)231,65428
Polymers227,9744
Non-polymers3,68024
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area13060 Å2
ΔGint-73 kcal/mol
Surface area72840 Å2
MethodPISA
2
C: Pyruvate kinase
D: Pyruvate kinase
hetero molecules

C: Pyruvate kinase
D: Pyruvate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)231,65428
Polymers227,9744
Non-polymers3,68024
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
Buried area13070 Å2
ΔGint-77 kcal/mol
Surface area72610 Å2
MethodPISA
3
G: Pyruvate kinase
H: Pyruvate kinase
hetero molecules

E: Pyruvate kinase
F: Pyruvate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)231,22626
Polymers227,9744
Non-polymers3,25222
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_444x-1/2,-y-1/2,-z-11
Buried area12740 Å2
ΔGint-66 kcal/mol
Surface area73160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)115.809, 403.204, 113.593
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

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Protein / Sugars , 2 types, 16 molecules ABCDEFGH

#1: Protein
Pyruvate kinase


Mass: 56993.590 Da / Num. of mol.: 8
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: 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.: 8 / Source method: obtained synthetically / Formula: C6H14O12P2
IdentifierTypeProgram
b-D-Fruf1PO36PO3IUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0

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Non-polymers , 5 types, 3887 molecules

#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-UDP / URIDINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 404.161 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C9H14N2O12P2 / Comment: UDP*YM
#5: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: K
#6: Chemical
ChemComp-OXL / OXALATE ION


Mass: 88.019 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2O4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3849 / 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: 2.91 Å3/Da / Density % sol: 57.71 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.3
Details: 60 mM HEPES pH7.3, 75 mM NaCl, 75 mM KCl, 10 mM MgCl2, 75 mM Na formate, 14 % PEG3350, 10 mM oxalate, 10 mM FBP, 5 mM 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
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: 1.89→48.17 Å / Num. obs: 423736 / % possible obs: 99.8 % / Redundancy: 13.34 % / CC1/2: 0.996 / Rmerge(I) obs: 0.062 / Rrim(I) all: 0.079 / Net I/σ(I): 6.23
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique obsCC1/2Rrim(I) allDiffraction-ID
1.89-20.307513870.8560.3991
2-2.140.211531400.9290.2741
2.14-2.310.152491690.960.1961
2.31-2.530.121439650.9720.1561
2.53-2.830.096364640.9820.1231
2.83-3.260.07309430.9890.0891
3.26-3.990.054251470.9920.0671
3.99-5.630.046182280.9940.0571
5.63-48.170.03398920.9980.041

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
XDSdata scaling
MOLREPphasing
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.89→48.16 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.958 / Cross valid method: THROUGHOUT / ESU R: 0.116 / ESU R Free: 0.116 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20472 21187 5 %RANDOM
Rwork0.16524 ---
obs0.16721 402543 99.75 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 36.73 Å2
Baniso -1Baniso -2Baniso -3
1-0.93 Å20 Å20 Å2
2--0.55 Å2-0 Å2
3----1.48 Å2
Refinement stepCycle: 1 / Resolution: 1.89→48.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms30720 0 406 3849 34975
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.01331462
X-RAY DIFFRACTIONr_bond_other_d0.0360.01730119
X-RAY DIFFRACTIONr_angle_refined_deg1.7191.6642504
X-RAY DIFFRACTIONr_angle_other_deg2.3461.58969849
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.74554000
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.68922.9851608
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.642155776
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.06215216
X-RAY DIFFRACTIONr_chiral_restr0.080.24332
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0235087
X-RAY DIFFRACTIONr_gen_planes_other0.0130.026093
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_it3.1313.58116024
X-RAY DIFFRACTIONr_mcbond_other3.1313.5816023
X-RAY DIFFRACTIONr_mcangle_it4.1525.35620016
X-RAY DIFFRACTIONr_mcangle_other4.1525.35720017
X-RAY DIFFRACTIONr_scbond_it4.424.11315438
X-RAY DIFFRACTIONr_scbond_other4.424.11415397
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.675.94922441
X-RAY DIFFRACTIONr_long_range_B_refined8.07344.07335811
X-RAY DIFFRACTIONr_long_range_B_other8.01743.37134787
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.89→1.936 Å
RfactorNum. reflection% reflection
Rfree0.303 1506 -
Rwork0.289 28618 -
obs--96.75 %

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