2LDB
STRUCTURE DETERMINATION AND REFINEMENT OF BACILLUS STEAROTHERMOPHILUS LACTATE DEHYDROGENASE
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | THE ENZYME WAS COCRYSTALLIZED IN THE PRESENCE OF THE COENZYME NAD AND THE ACTIVATOR FBP. THE NAD MOLECULE IS SITUATED AT THE LDH COENZYME BINDING SITE. ONE FBP MOLECULE BINDS ACROSS THE P-AXIS. THE P-AXIS INTERSECTS THE ACTIVATOR MOLECULE GIVING RISE TO A STATISTICAL DISORDER (OCCUPANCY 0.5) AS FBP HAS ONLY PSEUDO-TWO-FOLD SYMMETRY. ONE SULFATE (SO4 3) BINDS AT THE SUBSTRATE BINDING SITE. ANOTHER SULFATE (SO4 4) IS CLOSE TO THE R-AXIS INTERFACE. |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.78 | 55.71 |
Crystal Data
Unit Cell | |
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Length ( ? ) | Angle ( ? ) |
a = 86.8 | ¦Á = 90 |
b = 86.8 | ¦Â = 90 |
c = 356.6 | ¦Ã = 120 |
Symmetry | |
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Space Group | P 61 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Resolution (High) | Resolution (Low) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (Observed) | R-Work | R-Free | Mean Isotropic B | ||||||||||
X-RAY DIFFRACTION | 3 | 6 | 0.26 |
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] | |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
p_orthonormal_tor | 31.1 |
p_staggered_tor | 20.2 |
p_planar_tor | 5.8 |
p_scangle_it | 2.32 |
p_mcangle_it | 1.72 |
p_scbond_it | 1.36 |
p_mcbond_it | 0.96 |
p_multtor_nbd | 0.304 |
p_xhyhbond_nbd | 0.254 |
p_singtor_nbd | 0.249 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 9344 |
Nucleic Acid Atoms | |
Solvent Atoms | 50 |
Heterogen Atoms | 256 |
Software
Software | |
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Software Name | Purpose |
PROLSQ | refinement |