7TCM | pdb_00007tcm

Crystal Structure of aspartate-semialdehyde dehydrogenase from Acinetobacter baumannii in complex with NADP

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	7SKB	apo structure, pdb entry 7SKB

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.5	287	Molecular Dimensions/Calibre MCSG1 screen, condition B3: 200mM Ammonium acetate,100mM BisTris / HCl pH 5.5, 25% (w/V) PEG 3350: AcbaC.17885.a.B1.PW38925 at 18mg/ml + 3mM NADP: additionally soaked over night with 5mM NADP: tray 3420159 b5: 15% EG + soak: puck: xdl8-1.

Crystal Properties
Matthews coefficient	Solvent content
2.27	45.77

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 82.95	α = 90
b = 53.21	β = 102.358
c = 87.33	γ = 90

Symmetry
Space Group	P 1 21 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	RAYONIX MX-300	Beryllium Lenses	2021-11-21	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-F	0.97872	APS	21-ID-F

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim 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	1.95	50	97.4	0.043	0.05	0.998	18.42	3.498		53292			33.934

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.95	2	80.9		0.191	0.249	0.945	4.3	2.34

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	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	FREE R-VALUE	apo structure, pdb entry 7SKB	1.95	45.15	1.35	53273	2023	97.48	0.1528	0.1516	0.15	0.1842	0.18	0	36

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]

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	12.3101
f_angle_d	0.8217
f_chiral_restr	0.0542
f_bond_d	0.0068
f_plane_restr	0.0068

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5608
Nucleic Acid Atoms
Solvent Atoms	509
Heterogen Atoms	96

Software

Software
Software Name	Purpose
XDS	data reduction
XSCALE	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
PHASER	phasing
Coot	model building
PHENIX	model building

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.