2I5B | pdb_00002i5b

The crystal structure of an ADP complex of Bacillus subtilis pyridoxal kinase provides evidence for the parralel emergence of enzyme activity during evolution

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1UB0

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8.5	290	28% peg 4000, 0.17M sodium acetate trihydrate, 0.1M Tris HCL (pH 8.5), 10mM MgCl, 10mM ADP, VAPOR DIFFUSION, HANGING DROP, temperature 290K

Crystal Properties
Matthews coefficient	Solvent content
2.27	45.86

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 102.499	α = 90
b = 102.499	β = 90
c = 251.36	γ = 90

Symmetry
Space Group	P 41 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	MARRESEARCH		2005-05-09	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU	1.54

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym 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	2.8	94.916	99.4	0.131	0.131	5.7	3.7	33604	33604			50.3

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	2.8	2.95	99.9		0.475	0.475	1.7	3.8	4844

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	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	MOLECULAR REPLACEMENT	THROUGHOUT	1UB0	2.8	12.87	33305	33305	1688	99.43	0.225	0.225	0.222	0.22	0.274	0.27	RANDOM	31.436

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]
					-0.01

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.85
r_dihedral_angle_4_deg	25.038
r_dihedral_angle_3_deg	18.133
r_dihedral_angle_1_deg	6.295
r_scangle_it	1.936
r_angle_refined_deg	1.455
r_scbond_it	1.145
r_mcangle_it	0.991
r_mcbond_it	0.576
r_symmetry_hbond_refined	0.43

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.85
r_dihedral_angle_4_deg	25.038
r_dihedral_angle_3_deg	18.133
r_dihedral_angle_1_deg	6.295
r_scangle_it	1.936
r_angle_refined_deg	1.455
r_scbond_it	1.145
r_mcangle_it	0.991
r_mcbond_it	0.576
r_symmetry_hbond_refined	0.43
r_symmetry_vdw_refined	0.358
r_nbtor_refined	0.311
r_nbd_refined	0.219
r_xyhbond_nbd_refined	0.13
r_chiral_restr	0.094
r_bond_refined_d	0.011
r_gen_planes_refined	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	9932
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms	135

Software

Software
Software Name	Purpose
SCALA	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
MAR345	data collection
MOSFLM	data reduction
CCP4	data scaling
MOLREP	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.