2PUN

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
2.54	51.64

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 214.73	α = 90
b = 83.62	β = 90
c = 51.17	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	2004-11-09	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	2.3	105.41	99.3	0.069	15.4	7.5	39876	39577		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	2.3	2.36	98.4		0.263	6.6

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	2.3	51.17	39876	39577	2099	99.25	0.20423	0.20423	0.20154	0.25456	RANDOM	31.804

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]
-2.15			-1.22		3.37

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.421
r_dihedral_angle_3_deg	14.576
r_dihedral_angle_4_deg	12.438
r_dihedral_angle_1_deg	6.372
r_scangle_it	2.458
r_scbond_it	1.611
r_angle_refined_deg	1.468
r_mcangle_it	0.842
r_mcbond_it	0.481
r_symmetry_hbond_refined	0.366

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.421
r_dihedral_angle_3_deg	14.576
r_dihedral_angle_4_deg	12.438
r_dihedral_angle_1_deg	6.372
r_scangle_it	2.458
r_scbond_it	1.611
r_angle_refined_deg	1.468
r_mcangle_it	0.842
r_mcbond_it	0.481
r_symmetry_hbond_refined	0.366
r_symmetry_vdw_refined	0.311
r_nbtor_refined	0.302
r_nbd_refined	0.208
r_xyhbond_nbd_refined	0.173
r_chiral_restr	0.099
r_metal_ion_refined	0.053
r_bond_refined_d	0.013
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5937
Nucleic Acid Atoms
Solvent Atoms	347
Heterogen Atoms	115

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.