3VDM

Crystal Structure of VldE, the pseudo-glycosyltransferase which catalyzes non-glycosidic C-N coupling in Validamycin A biosynthesis

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8	298	100 mM Tris-HCl, pH 8.0, 20-35% PEG3350, VAPOR DIFFUSION, SITTING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.31	46.84

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 85.237	α = 90
b = 48.562	β = 91.88
c = 123.049	γ = 90

Symmetry
Space Group	P 1 2 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	ADSC QUANTUM 315		2011-07-18	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 24-ID-C	0.9479	APS	24-ID-C

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	1.98	122.983	98.1			70660	69317	2.7	2.7

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.98	2.08	91.8

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1.98	49.103	2.7	67391	66548	3559	98.75	0.18933	0.18754	0.22191	RANDOM	41.854

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]
-0.49		-0.44	0.31		0.15

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.673
r_dihedral_angle_4_deg	16.296
r_dihedral_angle_3_deg	15.149
r_dihedral_angle_1_deg	5.475
r_scangle_it	5.15
r_scbond_it	3.47
r_mcangle_it	2.124
r_angle_refined_deg	1.673
r_mcbond_it	1.372
r_chiral_restr	0.126

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.673
r_dihedral_angle_4_deg	16.296
r_dihedral_angle_3_deg	15.149
r_dihedral_angle_1_deg	5.475
r_scangle_it	5.15
r_scbond_it	3.47
r_mcangle_it	2.124
r_angle_refined_deg	1.673
r_mcbond_it	1.372
r_chiral_restr	0.126
r_bond_refined_d	0.022
r_gen_planes_refined	0.01

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7474
Nucleic Acid Atoms
Solvent Atoms	489
Heterogen Atoms

Software

Software
Software Name	Purpose
ADSC	data collection
PHENIX	model building
REFMAC	refinement
XDS	data reduction
XDS	data scaling
PHENIX	phasing

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.