2PUI

Structures of 5-methylthioribose kinase reveal substrate specificity and unusual mode of nucleotide binding

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	298	22% PEG 2000MME, 0.3M sodium acetate, 0.1M TrisHCl, 8mM CHAPS, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.53	51.44

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 213.78	α = 90
b = 83.53	β = 90
c = 51.24	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	IMAGE PLATE	RIGAKU RAXIS IV++	osmic	2005-06-17	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU RUH3R	1.5418

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	2.2	106.6	98.9	0.08	17.3	13.7	45236	44738		5

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.2	2.257	95.5		0.302	8	12.74

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	FOURIER SYNTHESIS	THROUGHOUT	2.2	65.82	45236	44738	2385	98.87	0.2012	0.2012	0.19872	0.24883	RANDOM	32.791

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]
-1.1			-1.14		2.24

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.665
r_dihedral_angle_3_deg	14.91
r_dihedral_angle_4_deg	12.767
r_dihedral_angle_1_deg	5.665
r_scangle_it	2.182
r_scbond_it	1.472
r_angle_refined_deg	1.404
r_mcangle_it	0.779
r_mcbond_it	0.443
r_symmetry_hbond_refined	0.345

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.665
r_dihedral_angle_3_deg	14.91
r_dihedral_angle_4_deg	12.767
r_dihedral_angle_1_deg	5.665
r_scangle_it	2.182
r_scbond_it	1.472
r_angle_refined_deg	1.404
r_mcangle_it	0.779
r_mcbond_it	0.443
r_symmetry_hbond_refined	0.345
r_nbtor_refined	0.303
r_nbd_refined	0.201
r_xyhbond_nbd_refined	0.165
r_symmetry_vdw_refined	0.145
r_chiral_restr	0.095
r_metal_ion_refined	0.074
r_bond_refined_d	0.012
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5769
Nucleic Acid Atoms
Solvent Atoms	471
Heterogen Atoms	87

Software

Software
Software Name	Purpose
REFMAC	refinement
d*TREK	data scaling
d*TREK	data reduction
CNS	phasing

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.