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- PDB-5hke: bile salt hydrolase from Lactobacillus salivarius -

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Basic information

Entry
Database: PDB / ID: 5hke
Titlebile salt hydrolase from Lactobacillus salivarius
ComponentsBile salt hydrolase
KeywordsHYDROLASE / conjugated bile salt acid hydrolase / NTN-HYDROLASE / BILE ACIDS / CBAH / BSH
Function / homology
Function and homology information


choloylglycine hydrolase / lipid metabolic process / hydrolase activity
Similarity search - Function
: / : / 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
PHOSPHATE ION / choloylglycine hydrolase
Similarity search - Component
Biological speciesLactobacillus salivarius (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsHu, X.-J.
CitationJournal: Acta Crystallogr F Struct Biol Commun / Year: 2016
Title: Crystal structure of bile salt hydrolase from Lactobacillus salivarius.
Authors: Xu, F. / Guo, F. / Hu, X.J. / Lin, J.
History
DepositionJan 14, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 11, 2016Provider: repository / Type: Initial release
Revision 1.1Apr 18, 2018Group: Data collection / Database references / Derived calculations
Category: citation / citation_author ...citation / citation_author / pdbx_prerelease_seq / pdbx_struct_oper_list
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed ..._citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Sep 27, 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.3Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,2346
Polymers75,8552
Non-polymers3804
Water7,206400
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5990 Å2
ΔGint-47 kcal/mol
Surface area26410 Å2
MethodPISA
2
A: Bile salt hydrolase
B: Bile salt hydrolase
hetero molecules

A: Bile salt hydrolase
B: Bile salt hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)152,46912
Polymers151,7094
Non-polymers7608
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_775-x+2,-y+2,z1
Buried area18840 Å2
ΔGint-125 kcal/mol
Surface area45960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.790, 87.356, 86.766
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: OCS / Beg label comp-ID: OCS / End auth comp-ID: LEU / End label comp-ID: LEU / Refine code: _ / Auth seq-ID: 2 - 323 / Label seq-ID: 2 - 323

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein Bile salt hydrolase


Mass: 37927.285 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactobacillus salivarius (bacteria) / Cell line: NRRL B-30514 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: J7H3P9, choloylglycine hydrolase
#2: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 400 / 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: 2.42 Å3/Da / Density % sol: 49.13 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.8
Details: 20% Polyethylene glycol 3350, 0.2M potassium dihydrogen phosphate pH 4.8

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944 / Detector: CCD / Date: May 1, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 54757 / % possible obs: 99.3 % / Redundancy: 5.7 % / Biso Wilson estimate: 13 Å2 / Rmerge(I) obs: 0.054 / Net I/σ(I): 28.9
Reflection shellResolution: 1.9→1.93 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.236 / Mean I/σ(I) obs: 4.91 / % possible all: 90

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2bjf

2bjf


Resolution: 1.9→45.5 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.95 / SU B: 2.414 / SU ML: 0.072 / Cross valid method: THROUGHOUT / ESU R: 0.126 / ESU R Free: 0.117 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18533 2619 4.8 %RANDOM
Rwork0.15155 ---
obs0.15315 52091 99.19 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 19.805 Å2
Baniso -1Baniso -2Baniso -3
1--0.22 Å20 Å20 Å2
2--0.77 Å2-0 Å2
3----0.54 Å2
Refinement stepCycle: 1 / Resolution: 1.9→45.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5058 0 20 400 5478
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.025265
X-RAY DIFFRACTIONr_bond_other_d0.0080.024862
X-RAY DIFFRACTIONr_angle_refined_deg1.8771.9597160
X-RAY DIFFRACTIONr_angle_other_deg1.391311194
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4745646
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.69225.318267
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.71115876
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.9931520
X-RAY DIFFRACTIONr_chiral_restr0.1210.2782
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.026086
X-RAY DIFFRACTIONr_gen_planes_other0.0060.021242
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_it1.8261.7212572
X-RAY DIFFRACTIONr_mcbond_other1.8081.722571
X-RAY DIFFRACTIONr_mcangle_it2.3262.5663222
X-RAY DIFFRACTIONr_mcangle_other2.3262.5673223
X-RAY DIFFRACTIONr_scbond_it3.2892.0962693
X-RAY DIFFRACTIONr_scbond_other3.2522.0892686
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.8872.9813927
X-RAY DIFFRACTIONr_long_range_B_refined5.93114.6296135
X-RAY DIFFRACTIONr_long_range_B_other5.91414.5436078
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 38740 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.08 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 1.899→1.948 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.218 213 -
Rwork0.194 3432 -
obs--91.47 %

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