3KAL | pdb_00003kal

Structure of homoglutathione synthetase from Glycine max in closed conformation with homoglutathione, ADP, a sulfate ion, and three magnesium ions bound

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
in silico model	Other		Homology model of the soybean enzyme generated with SWISS-MODEL from the structure of human GS (PDB entry 2HGS)

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		7	277	20% PEG3000, 0.1 M 3-(N-morpholino)-2-hydroxypropanesulfonic acid (MOPSO), pH 7, 0.2 M MgSO4, VAPOR DIFFUSION, HANGING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
3.53	65.14

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 115.7	α = 90
b = 115.7	β = 90
c = 101.76	γ = 120

Symmetry
Space Group	P 32

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 315r		2007-06-18	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL9-1		SSRL	BL9-1

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	1.9	29.3	97.2	0.051	17.4	3.8		116705			36.1

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)
	1.9	1.95	93.1		0.458	2.9	3.8

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	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	HOMOGLUTATHIONE SYNTHETASE WITH GAMMA- GLUTAMYLCYSTEINE BOUND	1.9	29.26	116705	113853	5992	100	0.2	0.197	0.2	0.25	0.25	RANDOM	36.11

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]
0.07	0.03		0.07		-0.1

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.578
r_dihedral_angle_4_deg	23.316
r_dihedral_angle_3_deg	19.185
r_dihedral_angle_1_deg	8.92
r_scangle_it	6.725
r_scbond_it	4.934
r_angle_refined_deg	3.459
r_mcangle_it	3.029
r_mcbond_it	2.212
r_chiral_restr	0.357
r_nbtor_refined	0.311
r_nbd_refined	0.262
r_xyhbond_nbd_refined	0.239
r_symmetry_vdw_refined	0.216
r_symmetry_hbond_refined	0.187
r_bond_refined_d	0.047
r_gen_planes_refined	0.018
r_metal_ion_refined	0.013
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7423
Nucleic Acid Atoms
Solvent Atoms	734
Heterogen Atoms	154

Software

Software
Software Name	Purpose
HKL-2000	data collection
PHASER	phasing
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling