2LDB

STRUCTURE DETERMINATION AND REFINEMENT OF BACILLUS STEAROTHERMOPHILUS LACTATE DEHYDROGENASE

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
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
Matthews coefficient	Solvent content
2.78	55.71

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 86.8	α = 90
b = 86.8	β = 90
c = 356.6	γ = 120

Symmetry
Space Group	P 61

Refinement

Statistics
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
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
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
p_chiral_restr	0.166
p_planar_d	0.046
p_angle_d	0.043
p_plane_restr	0.023
p_bond_d	0.019
p_angle_deg
p_hb_or_metal_coord
p_xyhbond_nbd
p_transverse_tor
p_special_tor

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	9344
Nucleic Acid Atoms
Solvent Atoms	50
Heterogen Atoms	256

Software

Software
Software Name	Purpose
PROLSQ	refinement