6U60 | pdb_00006u60

Crystal structure of prephenate dehydrogenase tyrA from Bacillus anthracis in complex with NAD and L-tyrosine

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3GGG

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	6.2	289	0.2 ul of 12 mg/ml protein in 20 mM HEPES pH 7.5, 150 mM NaCl, 5% Glycerol, 10 mM BME, 5 mM NAD and 20 mM Tyrosine were mixed with 0.2 ul of the MCSG Suite 2 condition #81 (0.1 M Potassium/Sodium phosphate pH=6.2, 0.2M Sodium chloride, 20% w/v PEG 1000) and equilibrated against 1.5 M NaCl solution in 96 Well 3 drop Crystallization Plate (Swissci). Before crystallization the protein was incubated with 1/50 v/v of 2 mg/ml chymotrypsin solution at 289 K for 3 hours

Crystal Properties
Matthews coefficient	Solvent content
2.22	44.52

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 106.85	α = 90
b = 81.003	β = 90
c = 83.597	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	CCD	MARMOSAIC 300 mm CCD	Beryllium Lenses	2015-04-18	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-G	0.97856	APS	21-ID-G

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	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	50	99.8	0.075	0.08	0.027	0.999	9.1	8.5		42991		-3	24.8

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.1	2.14	99.3		1.302	1.411	0.534	0.612	1.6	6.7

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	3GGG	2.1	36.48	38244	1975	93.44	0.1634	0.1605	0.17	0.2203	0.23	RANDOM	36.389

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]
-0.59			-0.2		0.8

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.322
r_dihedral_angle_3_deg	15.419
r_dihedral_angle_4_deg	15.163
r_dihedral_angle_1_deg	6.281
r_angle_refined_deg	1.484
r_angle_other_deg	1.352
r_chiral_restr	0.07
r_bond_refined_d	0.008
r_gen_planes_refined	0.007
r_bond_other_d	0.001

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.322
r_dihedral_angle_3_deg	15.419
r_dihedral_angle_4_deg	15.163
r_dihedral_angle_1_deg	6.281
r_angle_refined_deg	1.484
r_angle_other_deg	1.352
r_chiral_restr	0.07
r_bond_refined_d	0.008
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5703
Nucleic Acid Atoms
Solvent Atoms	370
Heterogen Atoms	80

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-3000	data scaling
PDB_EXTRACT	data extraction
HKL-3000	data reduction
MOLREP	phasing
Coot	model building
HKL-3000	phasing
SCALEPACK	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.