8BLS | pdb_00008bls

Structure of Lactobacillus salivarius (Ls) bile salt hydrolase(BSH) in complex with Glycocholate (GCA)

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5Y7P	Bile salt hydrolase from lactobacillus salivarius complex with glycocholic acid and cholic acid
experimental model	PDB	5HKE	HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	4.8	293	20% Polyethylene glycol 3350, 0.2M potassium dihydrogen phosphate pH 4.8

Crystal Properties
Matthews coefficient	Solvent content
2.24	45.11

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 84.01	α = 90
b = 94.09	β = 90.64
c = 166.974	γ = 90

Symmetry
Space Group	P 1 21 1

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	RIGAKU SATURN 944		2015-05-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU FR-E SUPERBRIGHT	1.54

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	94.9	0.066	12.5	2.7		143414

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	2.1	2.14	86.7		0.232		2.6

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	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	5HKE	2.1	28.4	135309	7902	94.59	0.14952	0.14668	0.16	0.19924	0.2	RANDOM	26.367

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]
0.01		-0.02			-0.01

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.733
r_dihedral_angle_4_deg	14.829
r_dihedral_angle_3_deg	14.344
r_dihedral_angle_1_deg	7.323
r_long_range_B_refined	5.677
r_long_range_B_other	5.62
r_scangle_other	4.355
r_mcangle_it	2.938
r_mcangle_other	2.937
r_scbond_it	2.911
r_scbond_other	2.91
r_mcbond_it	2.111
r_mcbond_other	2.105
r_angle_refined_deg	1.568
r_angle_other_deg	1.34
r_chiral_restr	0.075
r_bond_refined_d	0.01
r_gen_planes_refined	0.008
r_bond_other_d	0.001
r_gen_planes_other	0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	20210
Nucleic Acid Atoms
Solvent Atoms	1572
Heterogen Atoms	297

Software

Software
Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
iMOSFLM	data reduction
PHASER	phasing
PDB_EXTRACT	data extraction