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- PDB-5y7p: Bile salt hydrolase from lactobacillus salivarius complex with gl... -

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Basic information

Entry
Database: PDB / ID: 5y7p
TitleBile salt hydrolase from lactobacillus salivarius complex with glycocholic acid and cholic acid
ComponentsBile salt hydrolase
KeywordsHYDROLASE / CONJUGATED BILE SALT ACID HYDROLASE / NTN-HYDROLASE / BILE ACIDS / COMPLEX
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
CHOLIC ACID / GLYCOCHOLIC ACID / DI(HYDROXYETHYL)ETHER / PHOSPHATE ION / choloylglycine hydrolase
Similarity search - Component
Biological speciesLactobacillus salivarius (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsHu, X.-J.
CitationJournal: To Be Published
Title: Crystal structure of the bile salt hydrolase from lactobacillus salivarius complex with glycocholic acid and cholic acid
Authors: Xu, F. / Hu, X.-J. / Lin, J.
History
DepositionAug 17, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 22, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 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

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Assembly

Deposited unit
A: Bile salt hydrolase
B: Bile salt hydrolase
C: Bile salt hydrolase
D: Bile salt hydrolase
E: Bile salt hydrolase
F: Bile salt hydrolase
G: Bile salt hydrolase
H: Bile salt hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)307,83824
Polymers303,4188
Non-polymers4,42016
Water17,817989
1
A: Bile salt hydrolase
B: Bile salt hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,3817
Polymers75,8552
Non-polymers1,5275
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7980 Å2
ΔGint-16 kcal/mol
Surface area27400 Å2
MethodPISA
2
C: Bile salt hydrolase
D: Bile salt hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,7345
Polymers75,8552
Non-polymers8793
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6860 Å2
ΔGint-15 kcal/mol
Surface area26250 Å2
MethodPISA
3
E: Bile salt hydrolase
F: Bile salt hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,9276
Polymers75,8552
Non-polymers1,0724
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7500 Å2
ΔGint-17 kcal/mol
Surface area26430 Å2
MethodPISA
4
G: Bile salt hydrolase
H: Bile salt hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,7966
Polymers75,8552
Non-polymers9414
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7850 Å2
ΔGint-9 kcal/mol
Surface area26710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.010, 94.090, 166.974
Angle α, β, γ (deg.)90.00, 90.64, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 8 molecules ABCDEFGH

#1: Protein
Bile salt hydrolase


Mass: 37927.285 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactobacillus salivarius (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: J7H3P9

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Non-polymers , 7 types, 1005 molecules

#2: Chemical ChemComp-GCH / GLYCOCHOLIC ACID / N-CHOLYLGLYCINE


Mass: 465.623 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C26H43NO6
#3: Chemical
ChemComp-CHD / CHOLIC ACID


Mass: 408.571 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C24H40O5
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#6: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#7: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 989 / 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: 2.26 Å3/Da / Density % sol: 45.5 % / Description: shaft
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.8
Details: 20% polyethylene glycol 3350, 0.2 M potassium dihydrogen phosphate pH 4.8. Then crystal is soaked in this buffer containing 5 uM glycocholic acid for 4 hrs.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ DW / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944 / Detector: CCD / Date: Jul 27, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 143414 / % possible obs: 95.1 % / Redundancy: 5.3 % / Biso Wilson estimate: 18.4 Å2 / Rmerge(I) obs: 0.073 / Net I/σ(I): 12.7
Reflection shellResolution: 2.1→2.14 Å / Redundancy: 4.9 % / Num. unique obs: 6716 / % possible all: 89.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5HKE

5hke


Resolution: 2.1→28.5 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.934 / SU B: 4.575 / SU ML: 0.121 / Cross valid method: THROUGHOUT / ESU R: 0.236 / ESU R Free: 0.187 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2135 7338 5.1 %RANDOM
Rwork0.15994 ---
obs0.16268 135874 94.55 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.73 Å2
Baniso -1Baniso -2Baniso -3
1--2.19 Å20 Å2-1.28 Å2
2--2.58 Å2-0 Å2
3----0.36 Å2
Refinement stepCycle: 1 / Resolution: 2.1→28.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20630 0 309 989 21928
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0221432
X-RAY DIFFRACTIONr_bond_other_d0.0020.0219327
X-RAY DIFFRACTIONr_angle_refined_deg1.6821.97629132
X-RAY DIFFRACTIONr_angle_other_deg1.015345113
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.67352583
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.22325.421072
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.208153583
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.1511581
X-RAY DIFFRACTIONr_chiral_restr0.1030.23249
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0223749
X-RAY DIFFRACTIONr_gen_planes_other0.0020.024235
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_it2.3092.64710350
X-RAY DIFFRACTIONr_mcbond_other2.3062.64710343
X-RAY DIFFRACTIONr_mcangle_it3.3743.95812923
X-RAY DIFFRACTIONr_mcangle_other3.3743.95912924
X-RAY DIFFRACTIONr_scbond_it2.8612.95511082
X-RAY DIFFRACTIONr_scbond_other2.862.95511082
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.2474.30616210
X-RAY DIFFRACTIONr_long_range_B_refined5.71930.91823542
X-RAY DIFFRACTIONr_long_range_B_other5.70630.86523391
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.101→2.155 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.269 471 -
Rwork0.2 8971 -
obs--85.43 %

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