3KAL

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)
TypeSourceAccession CodeDetails
in silico modelOtherHomology model of the soybean enzyme generated with SWISS-MODEL from the structure of human GS (PDB entry 2HGS)

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1727720% 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 coefficientSolvent content
3.5365.14

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 115.7α = 90
b = 115.7β = 90
c = 101.76γ = 120
Symmetry
Space GroupP 32

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2007-06-18MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL9-1SSRLBL9-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.929.397.20.05117.43.811670536.1
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
1.91.9593.10.4582.93.8

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTHOMOGLUTATHIONE SYNTHETASE WITH GAMMA- GLUTAMYLCYSTEINE BOUND1.929.2611670511385359921000.20.1970.25RANDOM36.11
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]
0.070.030.07-0.1
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.578
r_dihedral_angle_4_deg23.316
r_dihedral_angle_3_deg19.185
r_dihedral_angle_1_deg8.92
r_scangle_it6.725
r_scbond_it4.934
r_angle_refined_deg3.459
r_mcangle_it3.029
r_mcbond_it2.212
r_chiral_restr0.357
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.578
r_dihedral_angle_4_deg23.316
r_dihedral_angle_3_deg19.185
r_dihedral_angle_1_deg8.92
r_scangle_it6.725
r_scbond_it4.934
r_angle_refined_deg3.459
r_mcangle_it3.029
r_mcbond_it2.212
r_chiral_restr0.357
r_nbtor_refined0.311
r_nbd_refined0.262
r_xyhbond_nbd_refined0.239
r_symmetry_vdw_refined0.216
r_symmetry_hbond_refined0.187
r_bond_refined_d0.047
r_gen_planes_refined0.018
r_metal_ion_refined0.013
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 AtomsNumber
Protein Atoms7423
Nucleic Acid Atoms
Solvent Atoms734
Heterogen Atoms154

Software

Software
Software NamePurpose
HKL-2000data collection
PHASERphasing
REFMACrefinement
XDSdata reduction
XSCALEdata scaling