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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 Mesaconic Acid
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 8.5 292 Protein: 8.5 mg/ml, 0.15M Sodium chloride, 0.02M Tris-HCl (pH 8.0), 2mM Mesaconic Acid;
Screen: PEGs II (D11), 0.2M Magnesium chloride, 0.1M Tris (pH 8.5), 30% (w/v) PEG 4000;
Cryo: Reservoir
Crystal Properties Matthews coefficient Solvent content 1.93 36.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 34.52 α = 90 b = 67.2 β = 106.47 c = 60.469 γ = 90
Symmetry Space Group P 1 21 1
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 1.32 30 98.6 0.089 0.089 0.103 0.051 0.997 14.5 3.7 61217 -3 9.1
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 1.32 1.34 99.9 0.771 0.771 0.895 0.445 0.575 2.1 3.6
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 1.32 29.7 58148 3012 98.42 0.15853 0.15757 0.1628 0.17727 0.1817 RANDOM 9.894
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] -0.03 -0.04 0.02 0.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 9.116 r_long_range_B_refined 4.95 r_long_range_B_other 4.695 r_dihedral_angle_1_deg 4.26 r_scangle_other 2.731 r_dihedral_angle_2_deg 2.518 r_scbond_other 1.69 r_scbond_it 1.689 r_angle_refined_deg 1.411 r_mcangle_other 1.344
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 9.116 r_long_range_B_refined 4.95 r_long_range_B_other 4.695 r_dihedral_angle_1_deg 4.26 r_scangle_other 2.731 r_dihedral_angle_2_deg 2.518 r_scbond_other 1.69 r_scbond_it 1.689 r_angle_refined_deg 1.411 r_mcangle_other 1.344 r_mcangle_it 1.342 r_mcbond_it 0.849 r_mcbond_other 0.824 r_angle_other_deg 0.485 r_chiral_restr 0.076 r_gen_planes_refined 0.017 r_gen_planes_other 0.015 r_bond_refined_d 0.004 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 2451 Nucleic Acid Atoms Solvent Atoms 451 Heterogen Atoms 12
Software Software Software Name Purpose REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling PHASER phasing