8AHR | pdb_00008ahr

Crystal structure of D-amino acid aminotransferase from Aminobacterium colombiense in holo form with PLP

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5MQZ

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		288	0.2 M Sodium nitrate, 0.1 M Bis-tris propane pH 6.5, 20% PEG 3350

Crystal Properties
Matthews coefficient	Solvent content
1.98	37.83

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 61.19	α = 90
b = 80.974	β = 90
c = 98.96	γ = 90

Symmetry
Space Group	P 21 21 21

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	DECTRIS PILATUS 6M		2021-10-11	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID23-1	0.97625	ESRF	ID23-1

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	1.9	43.78	98.1	0.081	0.094	0.047	0.998	11	3.9		38455

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	1.9	1.94	99.3		0.754	0.87	0.42	0.614		4

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	5MQZ	1.9	43.78	34694	1783	92.42	0.1921	0.1894	0.2	0.2446	0.25	RANDOM	32.811

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]
-2.09			3.8		-1.72

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.728
r_dihedral_angle_4_deg	14.675
r_dihedral_angle_3_deg	14.147
r_dihedral_angle_1_deg	8.013
r_angle_refined_deg	1.975
r_angle_other_deg	1.387
r_chiral_restr	0.109
r_bond_refined_d	0.015
r_gen_planes_refined	0.013
r_bond_other_d	0.005

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.728
r_dihedral_angle_4_deg	14.675
r_dihedral_angle_3_deg	14.147
r_dihedral_angle_1_deg	8.013
r_angle_refined_deg	1.975
r_angle_other_deg	1.387
r_chiral_restr	0.109
r_bond_refined_d	0.015
r_gen_planes_refined	0.013
r_bond_other_d	0.005
r_gen_planes_other	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4189
Nucleic Acid Atoms
Solvent Atoms	147
Heterogen Atoms	30

Software

Software
Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
PDB_EXTRACT	data extraction
DIALS	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.