8IAU

Crystal structure of Streptococcus pneumoniae pyruvate kinase in complex with oxalate and fructose 1,6-bisphosphate


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
in silico modelAlphaFold 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP4.229816.5% PEG300,50mM Na Acetate pH4.2, 10mM Na HEPES HCl pH7.5, 75mM NaCl, 10mM MgCl2, 50mM KCl, 10mM FBP, 10mM Oxalate
Crystal Properties
Matthews coefficientSolvent content
2.5351.3

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 73.442α = 88.95
b = 114.66β = 88.12
c = 140.705γ = 76.52
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16MMain beamline optics is a double-crystal monochromator and a horizontal focusing mirror.2022-04-21MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSPRING-8 BEAMLINE BL44XU0.900SPring-8BL44XU

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)CC (Half)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
1249.38970.080.0940.9978.853.6293893
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
122.120.91799999999999991.0750.598

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT249.382791921469596.950.202010.199660.24609RANDOM46.44
Temperature Factor Modeling
Anisotropic B[1][1]Anisotropic B[1][2]Anisotropic B[1][3]Anisotropic B[2][2]Anisotropic B[2][3]Anisotropic B[3][3]
1.542.050.050.35-0.02-0.94
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.825
r_dihedral_angle_4_deg19.688
r_dihedral_angle_3_deg17.862
r_long_range_B_refined10.202
r_long_range_B_other10.202
r_scangle_other8.233
r_dihedral_angle_1_deg7.01
r_mcangle_it6.075
r_mcangle_other6.075
r_scbond_it5.711
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.825
r_dihedral_angle_4_deg19.688
r_dihedral_angle_3_deg17.862
r_long_range_B_refined10.202
r_long_range_B_other10.202
r_scangle_other8.233
r_dihedral_angle_1_deg7.01
r_mcangle_it6.075
r_mcangle_other6.075
r_scbond_it5.711
r_scbond_other5.711
r_mcbond_it4.608
r_mcbond_other4.604
r_angle_other_deg2.371
r_angle_refined_deg1.769
r_chiral_restr0.079
r_bond_other_d0.036
r_bond_refined_d0.012
r_gen_planes_other0.012
r_gen_planes_refined0.009
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms29996
Nucleic Acid Atoms
Solvent Atoms916
Heterogen Atoms283

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata scaling
XDSdata reduction
MOLREPphasing