9BGR | pdb_00009bgr

X-ray structure of the aminotransferase from Vibrio vulnificus responsible for the biosynthesis of 2,3-diacetamido-4-amino-2,3,4-trideoxy-arabinose in the presence of its external aldimine with 2,3-diacetamido-4-amino-2,3,4-trideoxy-l-arabinose

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	9BGP

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6	293	protein incubated with 5.0 mM UDP-4-amino-2,3-diacetoamido-2,3,4-trideoxy-L-arabinose and 1.0 mM PLP. Precipitant: 15-20% (w/v) poly(ethylene glycol) 5000, 200 mM NaCl, and 100 mM MES (pH 6.0)

Crystal Properties
Matthews coefficient	Solvent content
2.24	45.07

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 52.958	α = 83
b = 53.048	β = 82.17
c = 70.267	γ = 74.36

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	PIXEL	Bruker PHOTON II		2024-02-23	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SEALED TUBE	BRUKER D8 QUEST	1.5418

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym 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	1.05	50	96.5	0.087	7.7	4.6		330200

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.05	1.15	87.6		0.481	1.8	2.1

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	FOURIER SYNTHESIS	THROUGHOUT	1.05	38.96	313419	16781	97.28	0.16028	0.15937	0.17	0.17728	0.18	RANDOM	8.476

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]
0.02	-0.02	-0.06	-0.03	0.07

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	14.976
r_dihedral_angle_2_deg	14.702
r_dihedral_angle_1_deg	6.456
r_rigid_bond_restr	4.787
r_long_range_B_refined	2.789
r_long_range_B_other	2.087
r_angle_refined_deg	1.663
r_scangle_other	1.304
r_scbond_it	0.99
r_scbond_other	0.99
r_mcangle_it	0.965
r_mcangle_other	0.965
r_mcbond_it	0.665
r_mcbond_other	0.665
r_angle_other_deg	0.528
r_chiral_restr	0.082
r_gen_planes_refined	0.009
r_bond_refined_d	0.008
r_gen_planes_other	0.002
r_bond_other_d
r_dihedral_angle_4_deg
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5671
Nucleic Acid Atoms
Solvent Atoms	956
Heterogen Atoms	204

Software

Software
Software Name	Purpose
REFMAC	refinement
SAINT	data reduction
SADABS	data scaling
REFMAC	phasing