5TJK
Crystal structure of GTA + A trisaccharide (native)
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1LZ0 |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 277 | Native crystals of GTA/GTB lacking any heavy metals were grown at 4 degrees Celsius from much higher concentrations of protein (30-40 mg/mL for GTB and 16-20 mg/mL for GTA) along with 1% PEG 4000, 4.5-5% 2-methyl-2,4-pentanediol (MPD), 100 mM ammonium sulfate, 70 mM sodium chloride, 50 mM ADA buffer pH 7.5, 30 mM sodium acetate buffer pH 4.6 and 5 mM MnCl2 for GTB crystallization and 5-8 mM CoCl2 for GTA crystallization. 10-15 microlitre drops were placed against a reservoir containing 3.7% PEG 4000, 7% MPD, 0.3 M ammonium sulfate, 0.25 M sodium chloride, 0.2 M ADA buffer and 0.1 M sodium acetate. The crystals were usually grown for 5-10 days. Before making complexes, crystals of GTA/GTB were washed with modified mother liquor ML-2 consisting of 3.5% PEG 4000, 50 mM ammonium sulfate, 40 mM sodium chloride, 35 mM ADA buffer and 15% MPD or glycerol. Crystals of native GTA/GTB in complex with the respective A or B trisaccharide were obtained by soaking them in mother liquor ML-2 with 15% glycerol or MPD and 45-50 mM of each substrate for 2-5 days at 4 degrees Celsius. Before freezing the crystals for data collection, the concentration of the cryoprotectant was made 30% glycerol or 20% MPD respectively |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.25 | 45.23 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 52.55 | α = 90 |
b = 148.66 | β = 90 |
c = 79.79 | γ = 90 |
Symmetry | |
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Space Group | C 2 2 21 |
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 | 113 | IMAGE PLATE | RIGAKU RAXIS IV++ | 2009-04-16 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | ROTATING ANODE | RIGAKU MICROMAX-002 | 1.5418 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | 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 | 1.45 | 19.69 | 99.1 | 0.036 | 0.036 | 17.7 | 4.27 | 55231 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
1 | 1.45 | 1.5 | 97.8 | 0.31 | 3.6 | 3.5 | 5382 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | 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 | THROUGHOUT | 1LZ0 | 1.45 | 19.69 | 52424 | 2805 | 99.04 | 0.1825 | 0.182 | 0.1927 | RANDOM | 21.194 |
Temperature Factor Modeling | ||||||
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Anisotropic B[1][1] | Anisotropic B[1][2] | Anisotropic B[1][3] | Anisotropic B[2][2] | Anisotropic B[2][3] | Anisotropic B[3][3] | |
-0.02 | 0.21 | -0.2 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 31.473 |
r_dihedral_angle_4_deg | 19.974 |
r_dihedral_angle_3_deg | 11.882 |
r_dihedral_angle_1_deg | 6.248 |
r_angle_refined_deg | 1.448 |
r_angle_other_deg | 0.973 |
r_chiral_restr | 0.086 |
r_bond_refined_d | 0.01 |
r_gen_planes_refined | 0.007 |
r_bond_other_d | 0.005 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2298 |
Nucleic Acid Atoms | |
Solvent Atoms | 202 |
Heterogen Atoms | 48 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
d*TREK | data scaling |
PDB_EXTRACT | data extraction |
d*TREK | data reduction |
PHASER | phasing |