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Crystal Structure of C4-Dicarboxylate-Binding Protein (PA0884) 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 9DTL
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 9 292 Protein: 8.5 mg/ml, 0.15M Sodium chloride, 0.02M Tris-HCl (pH 8.0), 2mM L-Malate;
Screen: PACT (D6), 0.1M MMT buffer pH 9.0, 25% (w/v) PEG 1500;
Cryo: Reservoir
Crystal Properties Matthews coefficient Solvent content 1.96 37.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 46.678 α = 90 b = 66.953 β = 90 c = 87.688 γ = 90
Symmetry Space Group P 21 21 21
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) Rrim I (All) 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 1.5 30 98.6 0.14 0.14 0.146 0.04 0.998 18.7 12.5 44360 -3 12.8
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.5 1.53 98.1 0.356 0.607 2.4 12.9
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 1.5 28.84 41929 2200 98.56 0.17648 0.17463 0.1756 0.21209 0.2132 RANDOM 16.349
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] 0.18 -1.12 0.94
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 8.938 r_long_range_B_refined 6.054 r_long_range_B_other 5.846 r_dihedral_angle_1_deg 4.667 r_scangle_other 3.702 r_scbond_other 2.357 r_scbond_it 2.356 r_dihedral_angle_2_deg 1.887 r_mcangle_other 1.576 r_mcangle_it 1.57
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 8.938 r_long_range_B_refined 6.054 r_long_range_B_other 5.846 r_dihedral_angle_1_deg 4.667 r_scangle_other 3.702 r_scbond_other 2.357 r_scbond_it 2.356 r_dihedral_angle_2_deg 1.887 r_mcangle_other 1.576 r_mcangle_it 1.57 r_angle_refined_deg 1.488 r_mcbond_it 1.047 r_mcbond_other 1.047 r_angle_other_deg 0.478 r_chiral_restr 0.078 r_gen_planes_refined 0.02 r_gen_planes_other 0.016 r_bond_refined_d 0.007 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2320 Nucleic Acid Atoms Solvent Atoms 354 Heterogen Atoms 9
Software Software Software Name Purpose REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling PHASER phasing