3NNT | pdb_00003nnt

Crystal Structure of K170M Mutant of Type I 3-Dehydroquinate Dehydratase (aroD) from Salmonella typhimurium LT2 in Non-Covalent Complex with Dehydroquinate.

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3LB0

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	3	295	Protein solution: 7.5 mG/mL, 0.25M Sodium chloride, 0.01M Tris pH 8.3, 2mM 3-Dehydroquinic acid (DHR); Screen solution: Classics F9, 0.05M Potassium phosphate, 20%(w/v) PEG 8000., VAPOR DIFFUSION, SITTING DROP, temperature 295K

Crystal Properties
Matthews coefficient	Solvent content
1.96	37.26

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 36.727	α = 91.18
b = 43.548	β = 101.27
c = 79.938	γ = 109.05

Symmetry
Space Group	P 1

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	2010-06-18	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)	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	1.6	30	96.7	0.03	23.2	2	58590	58590		-3	24

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)
	1.6	1.63	95		0.357	2.25	2	2852

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	3LB0	1.6	29.65	55405	55405	2950	96.75	0.15942	0.15942	0.1579	0.1654	0.18749	0.1914	RANDOM	19.535

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]
0.08	0.61	0.58	0.51	-0.25	0.03

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.046
r_dihedral_angle_4_deg	12.236
r_dihedral_angle_3_deg	9.683
r_scangle_it	4.498
r_dihedral_angle_1_deg	3.362
r_scbond_it	2.695
r_mcangle_it	1.667
r_angle_refined_deg	1.409
r_mcbond_it	0.96
r_angle_other_deg	0.85

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.046
r_dihedral_angle_4_deg	12.236
r_dihedral_angle_3_deg	9.683
r_scangle_it	4.498
r_dihedral_angle_1_deg	3.362
r_scbond_it	2.695
r_mcangle_it	1.667
r_angle_refined_deg	1.409
r_mcbond_it	0.96
r_angle_other_deg	0.85
r_mcbond_other	0.271
r_chiral_restr	0.08
r_bond_refined_d	0.011
r_gen_planes_refined	0.006
r_gen_planes_other	0.003
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3922
Nucleic Acid Atoms
Solvent Atoms	525
Heterogen Atoms	26

Software

Software
Software Name	Purpose
Blu-Ice	data collection
PHASER	phasing
REFMAC	refinement
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.