2PUP | pdb_00002pup

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, 10mM ATP, 2mM magnesium chloride, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.54	51.5

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 213.93	α = 90
b = 83.29	β = 90
c = 51.42	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	2007-02-15	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	2.6	107.21	98.3	0.098	9.8	4.9	27719	27245		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	2.6	2.667	99.6		0.358	3.4

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	FOURIER SYNTHESIS	THROUGHOUT	2.6	46.34	27719	27245	1450	98.29	0.21387	0.21387	0.21064	0.21	0.2741	0.28	RANDOM	35.827

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]
-1.45			-2.07		3.52

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.554
r_dihedral_angle_3_deg	16.515
r_dihedral_angle_4_deg	16.432
r_dihedral_angle_1_deg	6.223
r_scangle_it	2.567
r_scbond_it	1.664
r_angle_refined_deg	1.591
r_mcangle_it	0.921
r_mcbond_it	0.564
r_symmetry_vdw_refined	0.355

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.554
r_dihedral_angle_3_deg	16.515
r_dihedral_angle_4_deg	16.432
r_dihedral_angle_1_deg	6.223
r_scangle_it	2.567
r_scbond_it	1.664
r_angle_refined_deg	1.591
r_mcangle_it	0.921
r_mcbond_it	0.564
r_symmetry_vdw_refined	0.355
r_nbtor_refined	0.317
r_symmetry_hbond_refined	0.286
r_nbd_refined	0.225
r_metal_ion_refined	0.191
r_xyhbond_nbd_refined	0.174
r_chiral_restr	0.099
r_bond_refined_d	0.017
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5806
Nucleic Acid Atoms
Solvent Atoms	233
Heterogen Atoms	92

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 U.S. National Science Foundation (DBI-2321666), 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 R01GM157729.