4O8K | pdb_00004o8k

Crystal structure of Type III pantothenate kinase from Burkholderia thailandensis, apo structure

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4O5F	pdb entry 4O5F, pantothenate-bound structure, residues 85-150

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	290	Rigaku Reagents, JCSG+ c5: 800mM KH2PO4, 800mm Na2HPO4, 100mM HEPES/NaOH pH 7.5; ButhA.17924.a.A1.PD0391 at 20.0mg/ml, tray 251248c5, puck iyg6-15, cryo: 25% EG in two steps, VAPOR DIFFUSION, SITTING DROP, temperature 290K

Crystal Properties
Matthews coefficient	Solvent content
2.15	43

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 95.94	α = 90
b = 95.94	β = 90
c = 109.2	γ = 90

Symmetry
Space Group	P 43 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	CCD	ADSC QUANTUM 315r		2013-12-22	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 5.0.2	1.03320	ALS	5.0.2

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	1.7	50	99.3	0.043	0.043	24.85	7.1	56674	56269		-3	30.6

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	1.7	1.74	97.8		0.376	4.67

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	pdb entry 4O5F, pantothenate-bound structure, residues 85-150	1.7	50	56674	56234	2797	99.36	0.1631	0.1631	0.1619	0.17	0.1864	0.19	RANDOM	29.2943

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]
0.72			0.72		-1.45

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.375
r_dihedral_angle_4_deg	12.256
r_dihedral_angle_3_deg	11.614
r_dihedral_angle_1_deg	5.66
r_mcangle_it	2.167
r_angle_refined_deg	1.548
r_mcbond_it	1.393
r_mcbond_other	1.376
r_angle_other_deg	1.201
r_chiral_restr	0.092

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.375
r_dihedral_angle_4_deg	12.256
r_dihedral_angle_3_deg	11.614
r_dihedral_angle_1_deg	5.66
r_mcangle_it	2.167
r_angle_refined_deg	1.548
r_mcbond_it	1.393
r_mcbond_other	1.376
r_angle_other_deg	1.201
r_chiral_restr	0.092
r_bond_refined_d	0.013
r_gen_planes_refined	0.008
r_bond_other_d	0.006
r_gen_planes_other	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3635
Nucleic Acid Atoms
Solvent Atoms	400
Heterogen Atoms	30

Software

Software
Software Name	Purpose
XSCALE	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
BOS	data collection
XDS	data reduction

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.