6WZ6 | pdb_00006wz6

Complex of mutant (K173M) of Pseudomonas 7A Glutaminase-Asparaginase with L-Glu at pH 5. Covalent acyl-enzyme intermediate

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4PGA	PDB entry 4PGA

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5	293	0.2 M sodium malonate, pH 5.0, 20% w/v PEG3350

Crystal Properties
Matthews coefficient	Solvent content
2.41	48.99

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 78.63	α = 90
b = 130.463	β = 118.95
c = 81.414	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	PIXEL	DECTRIS EIGER X 16M		2019-08-09	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 22-ID	1.0	APS	22-ID

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	1.15	34.51	93	0.06	0.025	0.997	27.1	6.3		470476

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.15	1.18	53.9		0.428	0.26	0.808	2.3	3.2

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	PDB entry 4PGA	1.15	34.51	444163	3771	88.37	0.1	0.0998	0.1	0.1201	0.12	RANDOM	18.344

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]
-0.79		-0.09	-0.55		0.9

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.185
r_rigid_bond_restr	12.618
r_dihedral_angle_3_deg	12.4
r_dihedral_angle_4_deg	12.009
r_dihedral_angle_1_deg	6.461
r_angle_refined_deg	2.043
r_angle_other_deg	1.681
r_chiral_restr	0.129
r_bond_refined_d	0.018
r_gen_planes_refined	0.012

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.185
r_rigid_bond_restr	12.618
r_dihedral_angle_3_deg	12.4
r_dihedral_angle_4_deg	12.009
r_dihedral_angle_1_deg	6.461
r_angle_refined_deg	2.043
r_angle_other_deg	1.681
r_chiral_restr	0.129
r_bond_refined_d	0.018
r_gen_planes_refined	0.012
r_bond_other_d	0.005
r_gen_planes_other	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	9928
Nucleic Acid Atoms
Solvent Atoms	1795
Heterogen Atoms	48

Software

Software
Software Name	Purpose
HKL-3000	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-3000	data reduction
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.