1TKK

The Structure of a Substrate-Liganded Complex of the L-Ala-D/L-Glu Epimerase from Bacillus subtilis

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1JPM

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7	293	The protein was concentrated to 20 mg/ml and dialyzed against 5 mM HEPES, 2 mM MgCl2, 50 mM NaCl, 0.25 mM TCEP, 1 mM NaN3, pH 7.0, drop frozen as small pellets in liquid nitrogen and stored at -80 C. The frozen concentrated protein was thawed and diluted to 10 mg/mL with 5 mM HEPES, 2 mM MgCl2, 1 mM NaN3, pH 7.5. A stock solution of the peptide substrate L-Ala-L-Glu (Sigma) was neutralized to pH 7.5 with NaOH and brought to a final concentration of 1.6 M. This solution was added to the protein as 1/50th part by volume and the resultant mixture utilized for crystallization experiments. The initial crystals were grown by hanging drop by mixing 5 ?l of protein solution and 5 ?l of a solution containing 9-11% dimethyl-PEG 5000, 50 mM MOPS, 1% MPD, 1 mM NaN3, pH 7.0 and suspending the droplets over 600 ?l precipitant at 20 C, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.43	49.48

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 117.4	α = 90
b = 134.6	β = 90
c = 194.9	γ = 90

Symmetry
Space Group	P 21 21 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	150	CCD	CUSTOM-MADE		2001-03-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-ID	1.0	APS	19-ID

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	2.1	50	96.7	0.159	8.6	6.2	173946	173946

Highest Resolution Shell
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)
	2.1	2.18	96.7		0.508	2.6	6.4

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1JPM	2.1	30	173500	164780	8685	96.51	0.222	0.222	0.219	0.285	RANDOM	25.435

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]
-1.64			1.87		-0.23

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	5.733
r_scangle_it	3.933
r_mcangle_it	2.815
r_scbond_it	2.637
r_mcbond_it	1.967
r_angle_refined_deg	1.199
r_angle_other_deg	0.78
r_nbd_other	0.22
r_symmetry_hbond_refined	0.194
r_nbd_refined	0.192
r_symmetry_vdw_other	0.189
r_xyhbond_nbd_refined	0.172
r_symmetry_vdw_refined	0.155
r_nbtor_other	0.084
r_chiral_restr	0.068
r_bond_refined_d	0.01
r_gen_planes_refined	0.004
r_gen_planes_other	0.003
r_bond_other_d	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	21626
Nucleic Acid Atoms
Solvent Atoms	1521
Heterogen Atoms	120

Software

Software
Software Name	Purpose
REFMAC	refinement
d*TREK	data reduction
d*TREK	data scaling
MOLREP	phasing