1B48 | pdb_00001b48

CRYSTAL STRUCTURE OF MGSTA4-4 IN COMPLEX WITH GSH CONJUGATE OF 4-HYDROXYNONENAL IN ONE SUBUNIT AND GSH IN THE OTHER: EVIDENCE OF SIGNALING ACROSS DIMER INTERFACE IN MGSTA4-4


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1GUHPDB ENTRY 1GUH

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
17.5CRYSTALS WERE GROWN IN HANGING DROPS WHICH INITIALLY CONSISTED OF 0.11 MM PROTEIN IN 0.047 M HEPES BUFFER (PH 7.5) CONTAINING 1.82 MM GLUTATHIONE, 10.91 MM HNA-SG (GSH CONJUGATE OF 4-HYDROXYNONENAL), 9.1% ETHANOL, 4.5% ISOPROPANOL, AND 6.5% PEG MONOMETHYL ETHER 5K (PH 7.5). THE DROPS WERE EQUILIBRATED AT 293 K AGAINST WELL SOLUTION CONTAINING 10% ISOPROPANOL AND 12% PEG MONOMETHYL ETHER 5K IN 80 MM HEPES BUFFER (PH 7.5).
Crystal Properties
Matthews coefficientSolvent content
2.3547.6

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 114.45α = 90
b = 96.14β = 90
c = 50.84γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray293IMAGE PLATEMAC Science DIP-2020MIRRORS1997-05-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODEENRAF-NONIUS FR591

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge 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
12.62087.40.0751412.11564739
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
2.62.6960.10.2562.352.74

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (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 Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE RPDB ENTRY 1GUH2.62021564778187.40.2440.2440.230.317RANDOM49
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
KeyRefinement Restraint Deviation
x_dihedral_angle_d19.79
x_angle_deg1.364
x_improper_angle_d1.117
x_bond_d0.008
x_bond_d_na
x_bond_d_prot
x_angle_d
x_angle_d_na
x_angle_d_prot
x_angle_deg_na
RMS Deviations
KeyRefinement Restraint Deviation
x_dihedral_angle_d19.79
x_angle_deg1.364
x_improper_angle_d1.117
x_bond_d0.008
x_bond_d_na
x_bond_d_prot
x_angle_d
x_angle_d_na
x_angle_d_prot
x_angle_deg_na
x_angle_deg_prot
x_dihedral_angle_d_na
x_dihedral_angle_d_prot
x_improper_angle_d_na
x_improper_angle_d_prot
x_mcbond_it
x_mcangle_it
x_scbond_it
x_scangle_it
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3586
Nucleic Acid Atoms
Solvent Atoms40
Heterogen Atoms51

Software

Software
Software NamePurpose
AMoREphasing
X-PLORrefinement
HKL-2000data reduction
HKL-2000data scaling