2PU8 | pdb_00002pu8

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	51.59

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 213.81	α = 90
b = 83.24	β = 90
c = 51.57	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 optics	2005-06-18	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	2.1	107.2	97.5	0.067	14.4	7.2	54913	53540		3

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	2.1	2.154	96.1		0.276	6.2	7.4

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	2.1	65.68	52044	50785	2713	97.58	0.20273	0.20273	0.20014	0.2	0.25155	0.25	RANDOM	29.387

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]
-1.63			-1.47		3.09

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.343
r_dihedral_angle_3_deg	13.94
r_dihedral_angle_4_deg	13.739
r_dihedral_angle_1_deg	5.677
r_scangle_it	2.22
r_scbond_it	1.462
r_angle_refined_deg	1.263
r_mcangle_it	0.751
r_mcbond_it	0.446
r_nbtor_refined	0.301

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.343
r_dihedral_angle_3_deg	13.94
r_dihedral_angle_4_deg	13.739
r_dihedral_angle_1_deg	5.677
r_scangle_it	2.22
r_scbond_it	1.462
r_angle_refined_deg	1.263
r_mcangle_it	0.751
r_mcbond_it	0.446
r_nbtor_refined	0.301
r_symmetry_vdw_refined	0.192
r_nbd_refined	0.189
r_xyhbond_nbd_refined	0.166
r_symmetry_hbond_refined	0.132
r_chiral_restr	0.085
r_bond_refined_d	0.011
r_gen_planes_refined	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5845
Nucleic Acid Atoms
Solvent Atoms	473
Heterogen Atoms	29

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.