2Q7W | pdb_00002q7w

Structural Studies Reveals the Inactivation of E. coli L-aspartate aminotransferase (S)-4,5-amino-dihydro-2-thiophenecarboxylic acid (SADTA) via two mechanisms at pH 6.0

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1AMQ	PDB ENTRY 1AMQ

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	EVAPORATION	6	298	25 mM potassium phosphate, 43% saturated ammonium sulfate, 20 mM SADTA, pH 6.0, EVAPORATION, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.96	58.51

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 153.623	α = 90
b = 85.135	β = 90
c = 78.849	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	100	CCD	ADSC QUANTUM 315		2005-02-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 14-BM-C	0.9	APS	14-BM-C

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	1.4	77	97	0.062	17.4	5.7		93239

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	1.4	1.45	99.8		0.571	2.7	5.4	10020

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (I)	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	PDB ENTRY 1AMQ	1.4	76.92	2	93239	4903	96.42	0.15556	0.15386	0.15	0.18836	0.19	RANDOM	23.351

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]
-1.03			0.32		0.71

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.75
r_dihedral_angle_4_deg	18.82
r_dihedral_angle_3_deg	13.056
r_scangle_it	5.887
r_dihedral_angle_1_deg	5.86
r_scbond_it	4.361
r_mcangle_it	2.847
r_mcbond_it	1.995
r_angle_refined_deg	1.923
r_nbtor_refined	0.319

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.75
r_dihedral_angle_4_deg	18.82
r_dihedral_angle_3_deg	13.056
r_scangle_it	5.887
r_dihedral_angle_1_deg	5.86
r_scbond_it	4.361
r_mcangle_it	2.847
r_mcbond_it	1.995
r_angle_refined_deg	1.923
r_nbtor_refined	0.319
r_nbd_refined	0.256
r_symmetry_hbond_refined	0.252
r_symmetry_vdw_refined	0.234
r_xyhbond_nbd_refined	0.218
r_chiral_restr	0.115
r_bond_refined_d	0.016
r_gen_planes_refined	0.01

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2947
Nucleic Acid Atoms
Solvent Atoms	428
Heterogen Atoms	111

Software

Software
Software Name	Purpose
REFMAC	refinement
ADSC	data collection
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	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.