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Crystal Structure of C4-Dicarboxylate-Binding Periplasmic Protein (PA5167) of Tripartite ATP-independent Periplasmic Transporter Family from Pseudomonas aeruginosa PAO1 in Complex with L-Malate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 9DSY
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6 292 Protein: 7.0 mg/ml, 0.5M Sodium chloride, 0.02M Tris-HCl (pH 8.0), 2mM L-Malate;
Screen: PACT (B8), 0.2 M Ammonium chloride, 0.1 M MES (pH 6.0), 20% (w/v) PEG 6000;
Cryo: Reservoir
Crystal Properties Matthews coefficient Solvent content 1.96 37.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 34.505 α = 78.95 b = 44.532 β = 84.44 c = 46.886 γ = 75.84
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 9M 2022-10-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-D 1.12723 APS 21-ID-D
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 1.3 30 87.3 0.047 0.047 0.028 0.997 25.2 3.7 56875 -3 11.6
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.3 1.32 71.6 0.371 0.371 0.432 0.221 0.898 4.9 3.7
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 1.3 29.84 53993 2880 87.15 0.14167 0.14026 0.1501 0.16739 0.1759 RANDOM 18.43
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] -0.39 -0.15 -0.03 -0.96 0.31 1.4
RMS Deviations Key Refinement Restraint Deviation r_long_range_B_refined 12.965 r_long_range_B_other 11.942 r_dihedral_angle_3_deg 8.276 r_scangle_other 7.455 r_mcangle_other 5.907 r_mcangle_it 5.905 r_scbond_other 4.939 r_scbond_it 4.938 r_dihedral_angle_1_deg 4.524 r_mcbond_it 4.057
RMS Deviations Key Refinement Restraint Deviation r_long_range_B_refined 12.965 r_long_range_B_other 11.942 r_dihedral_angle_3_deg 8.276 r_scangle_other 7.455 r_mcangle_other 5.907 r_mcangle_it 5.905 r_scbond_other 4.939 r_scbond_it 4.938 r_dihedral_angle_1_deg 4.524 r_mcbond_it 4.057 r_mcbond_other 4.048 r_dihedral_angle_2_deg 2.573 r_rigid_bond_restr 2.007 r_angle_refined_deg 1.349 r_angle_other_deg 0.474 r_chiral_restr 0.074 r_gen_planes_refined 0.01 r_gen_planes_other 0.008 r_bond_refined_d 0.005 r_bond_other_d 0.001 r_dihedral_angle_4_deg r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2420 Nucleic Acid Atoms Solvent Atoms 270 Heterogen Atoms 14
Software Software Software Name Purpose REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling PHASER phasing