2FM7 | pdb_00002fm7

Evolution of Enzymatic Activity in the Tautomerase Superfamily: Mechanistic and Structural Consequences of the L8R Mutation in 4-Oxalocrotonate Tautomerase

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1BJP	PDB entry 1BJP with coordinates for OXP removed

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	298	3 microlitres of protein (20 mg/mL solution in 10 mM Tris-Cl, pH 7.0) mixed with an equal volume of reservoir buffer [30% O-(2-aminopropyl)-O-(2-methoxyethyl)polypropylene glycol 500, 100 mM 2-(N-morpholino)ethanesulfonic acid, pH 6.5, and 50 mM CsCl]. The resulting mixture was allowed to equilibrate against 50 microlitres of reservoir solution, VAPOR DIFFUSION, SITTING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.72	54.78

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 80.863	α = 90
b = 80.863	β = 90
c = 117.038	γ = 120

Symmetry
Space Group	P 63

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	IMAGE PLATE	RIGAKU RAXIS HTC		2004-02-27	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU RU300	1.5418

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym 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	2.8	50	99.9	0.12	0.162	5.7	7.8	10782	10209		2	35.1

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.8	2.9	100		0.401	0.424		7.7

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB entry 1BJP with coordinates for OXP removed	2.8	34	10726	10209	514	99.97	0.23327	0.23327	0.22979	0.23	0.30109	0.29	RANDOM	25.763

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]
1.3	0.65		1.3		-1.95

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	5.983
r_scangle_it	5.885
r_scbond_it	3.186
r_angle_refined_deg	2.357
r_mcangle_it	2.338
r_mcbond_it	1.257
r_xyhbond_nbd_refined	0.325
r_symmetry_vdw_refined	0.291
r_nbd_refined	0.248
r_chiral_restr	0.115

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	5.983
r_scangle_it	5.885
r_scbond_it	3.186
r_angle_refined_deg	2.357
r_mcangle_it	2.338
r_mcbond_it	1.257
r_xyhbond_nbd_refined	0.325
r_symmetry_vdw_refined	0.291
r_nbd_refined	0.248
r_chiral_restr	0.115
r_symmetry_hbond_refined	0.096
r_bond_refined_d	0.024
r_gen_planes_refined	0.017

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2769
Nucleic Acid Atoms
Solvent Atoms	199
Heterogen Atoms	1

Software

Software
Software Name	Purpose
HKL-2000	data collection
SCALEPACK	data scaling
MOLREP	phasing
REFMAC	refinement
HKL-2000	data reduction

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.