3T4U | pdb_00003t4u

L29I Mutation in an Aryl Esterase from Pseudomonas fluorescens Leads to Unique Peptide Flip and Increased Activity

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1VA4	PDB ENTRY 1VA4

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	293	1% PEG 400, 1.65M (NH4)2SO4, 0.1M HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
4.39	71.98

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 145.883	α = 90
b = 145.883	β = 90
c = 128.587	γ = 120

Symmetry
Space Group	P 32

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	CCD	NOIR-1	mirrors	2008-05-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 4.2.2	0.98	ALS	4.2.2

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	2.02	50	98.7	0.106	5.7	3.01		200730	1	3	17.3

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)
1	2.02	2.09	97.6		0.237	2.9	2.77	19582

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (I)	Cut-off Sigma (F)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	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 1VA4	2.02	48.23	3	1	198019	9963	98.65	0.1939	0.1924	0.1946	0.2213	0.2227	RANDOM	21.1125

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]
0.1	0.05		0.1		-0.16

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.961
r_dihedral_angle_4_deg	17.824
r_dihedral_angle_3_deg	13.553
r_dihedral_angle_1_deg	5.538
r_scangle_it	3.189
r_scbond_it	2.056
r_angle_refined_deg	1.39
r_mcangle_it	1.234
r_mcbond_it	0.716
r_chiral_restr	0.109

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.961
r_dihedral_angle_4_deg	17.824
r_dihedral_angle_3_deg	13.553
r_dihedral_angle_1_deg	5.538
r_scangle_it	3.189
r_scbond_it	2.056
r_angle_refined_deg	1.39
r_mcangle_it	1.234
r_mcbond_it	0.716
r_chiral_restr	0.109
r_bond_refined_d	0.016
r_gen_planes_refined	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	12720
Nucleic Acid Atoms
Solvent Atoms	1273
Heterogen Atoms	195

Software

Software
Software Name	Purpose
d*TREK	data scaling
SCALEPACK	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
d*TREK	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.