8ZLY

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

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	8XW9

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.3	298	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

Crystal Properties
Matthews coefficient	Solvent content
2.91	57.71

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 115.809	α = 90
b = 403.204	β = 90
c = 113.593	γ = 90

Symmetry
Space Group	P 21 21 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	PIXEL	DECTRIS EIGER X 16M	Main beamline optics is a double-crystal monochromator and a horizontal focusing mirror	2023-12-04	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL44XU	0.900	SPring-8	BL44XU

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)	Redundancy	Number Reflections (All)	Number Reflections (Observed)	Observed Criterion Sigma (F)	Observed Criterion Sigma (I)	B (Isotropic) From Wilson Plot
1	1.89	48.17	99.8	0.062	0.079	0.996	6.23	13.34		423736

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)	Redundancy	Number Unique Reflections (All)
1	1.89	2			0.307	0.399	0.856

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1.89	48.16	402543	21187	99.75	0.16721	0.16524	0.20472	RANDOM	36.73

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]
0.93			0.55		-1.48

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.689
r_dihedral_angle_4_deg	17.062
r_dihedral_angle_3_deg	14.642
r_long_range_B_refined	8.073
r_long_range_B_other	8.017
r_dihedral_angle_1_deg	6.745
r_scangle_other	6.67
r_scbond_it	4.42
r_scbond_other	4.42
r_mcangle_it	4.152
r_mcangle_other	4.152
r_mcbond_it	3.131
r_mcbond_other	3.131
r_angle_other_deg	2.346
r_angle_refined_deg	1.719
r_chiral_restr	0.08
r_bond_other_d	0.036
r_gen_planes_other	0.013
r_bond_refined_d	0.011
r_gen_planes_refined	0.009
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 Atoms	Number
Protein Atoms	30720
Nucleic Acid Atoms
Solvent Atoms	3849
Heterogen Atoms	406

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data scaling
MOLREP	phasing
XDS	data reduction