8DP2
Crystal Structure of UDP-N-acetylmuramoylalanine--D-glutamate ligase (MurD) from Pseudomonas aeruginosa PAO1 in complex with UMA (Uridine-5'-diphosphate-N-acetylmuramoyl-L-Alanine)
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 7U35 | ADP-bound MurD, pdb entry 7U35, in three domains |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 7.5 | 287 | RigakuReagents JCSG Top96 screen, condition b1: 100mM HEPES free acid / sodium hydroxide pH 7.5, 30% (V/V) PEG 400, 5% (w/V) PEG 3000, 10% (V/V) Glycerol: PsaeA.17938.a.B2.PS38065 at 40mg/ml + 3mM UMA (BSI102034) and MgCl2: tray: 325018b1: cryo: direct, puck: tua1-2. SIN is modeled tenatively based on density only, it was not added to the crystallizaton buffer |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.72 | 54.8 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 95.46 | α = 90 |
b = 95.46 | β = 90 |
c = 99.55 | γ = 120 |
Symmetry | |
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Space Group | P 61 |
Diffraction
Diffraction Experiment | ||||||||||||||
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ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
1 | 1 | x-ray | 100 | CCD | RAYONIX MX-300 | 2022-06-09 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 21-ID-F | 0.97872 | APS | 21-ID-F |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | Rrim 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 | 1.6 | 50 | 100 | 0.056 | 0.06 | 0.999 | 20.91 | 8.964 | 67812 | 28.069 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||
1 | 1.6 | 1.64 | 100 | 0.593 | 0.653 | 0.809 | 2.31 | 5.831 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Cut-off Sigma (F) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | |||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | FREE R-VALUE | ADP-bound MurD, pdb entry 7U35, in three domains | 1.6 | 41.34 | 1.35 | 67742 | 1964 | 99.99 | 0.1506 | 0.15 | 0.1689 | 0 | 25.91 |
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 | |
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Key | Refinement Restraint Deviation |
f_dihedral_angle_d | 14.4935 |
f_angle_d | 1.0479 |
f_chiral_restr | 0.0688 |
f_plane_restr | 0.0091 |
f_bond_d | 0.0089 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 3374 |
Nucleic Acid Atoms | |
Solvent Atoms | 516 |
Heterogen Atoms | 104 |
Software
Software | |
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Software Name | Purpose |
XDS | data reduction |
XSCALE | data scaling |
PHENIX | refinement |
PDB_EXTRACT | data extraction |
PHASER | phasing |