3PXU | pdb_00003pxu

Crystal structure of phosphopantetheine adenylyltransferase from Burkholderia pseudomallei bound to dephospho-coenzyme A

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1B6T	1B6T molecule A, protein only

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7	298	Hampton Crystal Screen condition c8, 2.0 M ammonium sulfate, 5.5 mg/mL protein with expression tag removed, crystal tracking ID 203611c8, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 289K, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.67	53.91

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 134.161	α = 90
b = 134.161	β = 90
c = 134.161	γ = 90

Symmetry
Space Group	I 4 3 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	RIGAKU SATURN 944+		2009-08-04	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU FR-E+ SUPERBRIGHT	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	2.05	50	99	0.087	44.5	23.2		13128

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	2.18	98.1		0.519	6.57	22.4	1181

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	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	1B6T molecule A, protein only	2.1	28.6	12286	620	99.4	0.2016	0.1995	0.2	0.2419	0.22	RANDOM	29.9984

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]

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.607
r_dihedral_angle_4_deg	17.106
r_dihedral_angle_3_deg	14.504
r_dihedral_angle_1_deg	5.26
r_scangle_it	4.257
r_scbond_it	2.584
r_mcangle_it	1.549
r_angle_refined_deg	1.463
r_mcbond_it	0.854
r_chiral_restr	0.095

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.607
r_dihedral_angle_4_deg	17.106
r_dihedral_angle_3_deg	14.504
r_dihedral_angle_1_deg	5.26
r_scangle_it	4.257
r_scbond_it	2.584
r_mcangle_it	1.549
r_angle_refined_deg	1.463
r_mcbond_it	0.854
r_chiral_restr	0.095
r_bond_refined_d	0.015
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1227
Nucleic Acid Atoms
Solvent Atoms	89
Heterogen Atoms	66

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
StructureStudio	data collection
HKL-2000	data reduction
HKL-2000	data scaling

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.