2PUL | pdb_00002pul

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	51.51

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 214.15	α = 90
b = 83.47	β = 90
c = 51.26	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	2004-04-27	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	105.41	99.8	0.072	14.3	7.6	59970	59838		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)
	2	2.052	99.7		0.339	5.3	7.24

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	65.8	59970	59838	3191	99.78	0.20527	0.20527	0.20339	0.22	0.24012	0.25	RANDOM	26.468

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]
-1.33			-0.86		2.19

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.849
r_dihedral_angle_3_deg	13.99
r_dihedral_angle_4_deg	12.389
r_dihedral_angle_1_deg	7.472
r_scangle_it	2.625
r_scbond_it	1.746
r_angle_refined_deg	1.422
r_mcangle_it	0.928
r_mcbond_it	0.563
r_nbtor_refined	0.303

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.849
r_dihedral_angle_3_deg	13.99
r_dihedral_angle_4_deg	12.389
r_dihedral_angle_1_deg	7.472
r_scangle_it	2.625
r_scbond_it	1.746
r_angle_refined_deg	1.422
r_mcangle_it	0.928
r_mcbond_it	0.563
r_nbtor_refined	0.303
r_nbd_refined	0.198
r_xyhbond_nbd_refined	0.165
r_symmetry_vdw_refined	0.151
r_symmetry_hbond_refined	0.127
r_chiral_restr	0.096
r_bond_refined_d	0.013
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5881
Nucleic Acid Atoms
Solvent Atoms	488
Heterogen Atoms	93

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.