7ROO | pdb_00007roo

Crystal structure of Friedel-Crafts alkylating enzyme CylK from Cylindospermum licheniforme with bromide

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	7RON

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7	298	Prior to crystallization trials, purified CylK protein in storage buffer (20 mM HEPES pH 7.8, 50 mM NaCl, 10 mM MgCl2, 10 mM CaCl2, 10% glycerol) was combined with 5-undecylbenzene-1,3-diol (UDR), a substrate analog dissolved in protein storage buffer containing 22% DMSO. The final protein solution contained 10 mg/mL CylK and 1.66 mM UDR. Crystals of undecylresorcinol-bound CylK were obtained by using the hanging drop vapor diffusion method in 2 uL drops mixed in 1:1 ratio with a precipitant solution of 1.8 M sodium malonate, pH 7.0. Crystals formed within about 1 week at room temperature. CylK crystals were soaked in 2 M sodium malonate with 500 mM NaBr for up to 1 min

Crystal Properties
Matthews coefficient	Solvent content
2.15	42.91

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 93.47	α = 90
b = 138.656	β = 90
c = 99.511	γ = 90

Symmetry
Space Group	C 2 2 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	80	CCD	MARMOSAIC 300 mm CCD		2020-07-09	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-G	0.97857	APS	21-ID-G

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	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	1.52	50	99.7	0.99	23.3	7		98866

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.52	1.55			0.843	2.14	5.5

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	7RON	1.52	46.78	89122	4649	94.63	0.1708	0.1693	0.18	0.1978	0.2	RANDOM	15.772

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]
0.14			-0.18		0.03

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.661
r_dihedral_angle_4_deg	20.541
r_dihedral_angle_3_deg	12.318
r_dihedral_angle_1_deg	7.253
r_angle_refined_deg	1.823
r_angle_other_deg	1.554
r_chiral_restr	0.091
r_bond_refined_d	0.013
r_gen_planes_refined	0.011
r_bond_other_d	0.001

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.661
r_dihedral_angle_4_deg	20.541
r_dihedral_angle_3_deg	12.318
r_dihedral_angle_1_deg	7.253
r_angle_refined_deg	1.823
r_angle_other_deg	1.554
r_chiral_restr	0.091
r_bond_refined_d	0.013
r_gen_planes_refined	0.011
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4978
Nucleic Acid Atoms
Solvent Atoms	403
Heterogen Atoms	45

Software

Software
Software Name	Purpose
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
REFMAC	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.