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- PDB-6a8t: E269A mutant of highly active EfBSH -

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Basic information

Entry
Database: PDB / ID: 6a8t
TitleE269A mutant of highly active EfBSH
ComponentsBile salt hydrolase
KeywordsHYDROLASE / Ntn / Bile Salt Hydrolase / Gut Microbiome
Function / homology
Function and homology information


: / Penicillin V Acylase; Chain A / Penicillin V Acylase; Chain A / Choloylglycine hydrolase/NAAA C-terminal / Linear amide C-N hydrolases, choloylglycine hydrolase family / Nucleophile aminohydrolases, N-terminal / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesEnterococcus faecalis T2 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsRamasamy, S. / Yadav, Y.
Funding support India, 1items
OrganizationGrant numberCountry
Council of Scientific & Industrial Research India
Citation
Journal: To Be Published
Title: E269A mutant of highly active EfBSH
Authors: Ramasamy, S. / Yadav, Y.
#1: Journal: To Be Published
Title: E269A mutant of highly active Bile salt Hydrolase from Enterococcus faecalis
Authors: Ramasamy, S. / Yadav, Y.
History
DepositionJul 10, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 10, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 25, 2019Group: Data collection / Category: reflns_shell
Item: _reflns_shell.Rmerge_I_obs / _reflns_shell.pdbx_Rpim_I_all / _reflns_shell.pdbx_Rrim_I_all
Revision 1.2Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Bile salt hydrolase
B: Bile salt hydrolase
C: Bile salt hydrolase
D: Bile salt hydrolase


Theoretical massNumber of molelcules
Total (without water)150,4244
Polymers150,4244
Non-polymers00
Water6,377354
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19100 Å2
ΔGint-79 kcal/mol
Surface area45710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.840, 156.320, 73.150
Angle α, β, γ (deg.)90.00, 98.88, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Bile salt hydrolase


Mass: 37605.969 Da / Num. of mol.: 4 / Mutation: E269A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterococcus faecalis T2 (bacteria) / Gene: EFBG_01849
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: C7CXJ5
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 354 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.3 Å3/Da / Density % sol: 46.47 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 0.14 M CaCl2, 0.07M CH3COONa pH-4.6, 14% v/v isopropanol.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: RRCAT INDUS-2 / Beamline: PX-BL21 / Wavelength: 0.9795 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Aug 7, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.1→41.14 Å / Num. obs: 77248 / % possible obs: 100 % / Redundancy: 12 % / CC1/2: 0.978 / Rmerge(I) obs: 0.219 / Rpim(I) all: 0.131 / Rrim(I) all: 0.255 / Net I/σ(I): 3.8
Reflection shellResolution: 2.1→2.1 Å / CC1/2: 0.984

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Processing

Software
NameVersionClassification
REFMAC5.8.0222refinement
iMOSFLMdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4WL3

4wl3


Resolution: 2.1→41.18 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.891 / Cross valid method: THROUGHOUT / ESU R: 0.259 / ESU R Free: 0.203 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24787 3706 4.8 %RANDOM
Rwork0.20343 ---
obs0.20559 73391 99.83 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 15.146 Å2
Baniso -1Baniso -2Baniso -3
1-1.04 Å20 Å2-2.19 Å2
2---0.74 Å20 Å2
3---0.37 Å2
Refinement stepCycle: 1 / Resolution: 2.1→41.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10372 0 0 354 10726
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.01510651
X-RAY DIFFRACTIONr_bond_other_d0.0010.0179320
X-RAY DIFFRACTIONr_angle_refined_deg1.4031.74114450
X-RAY DIFFRACTIONr_angle_other_deg3.6391.73521858
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.48851304
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.66122.883489
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.008151619
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.9971540
X-RAY DIFFRACTIONr_chiral_restr0.0670.21372
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0212028
X-RAY DIFFRACTIONr_gen_planes_other0.0080.022088
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0181.4835180
X-RAY DIFFRACTIONr_mcbond_other1.0181.4835181
X-RAY DIFFRACTIONr_mcangle_it1.7252.2226472
X-RAY DIFFRACTIONr_mcangle_other1.7252.2226473
X-RAY DIFFRACTIONr_scbond_it1.2711.6245471
X-RAY DIFFRACTIONr_scbond_other1.2711.6245470
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.1012.3757971
X-RAY DIFFRACTIONr_long_range_B_refined3.0216.99511611
X-RAY DIFFRACTIONr_long_range_B_other3.00616.98911568
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.1→2.155 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.319 262 -
Rwork0.269 5430 -
obs--99.82 %

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