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- PDB-2hez: Bifidobacterium longum bile salt hydrolase -

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Basic information

Entry
Database: PDB / ID: 2hez
TitleBifidobacterium longum bile salt hydrolase
ComponentsBile salt hydrolase
KeywordsHYDROLASE / alpha / beta
Function / homology
Function and homology information


chenodeoxycholoyltaurine hydrolase / chenodeoxycholoyltaurine hydrolase activity / choloylglycine hydrolase activity / choloylglycine hydrolase / bile acid biosynthetic process / Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / peptidoglycan-based cell wall / transferase 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
Bile salt hydrolase/transferase
Similarity search - Component
Biological speciesBifidobacterium longum (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsSuresh, C.G. / Kumar, R.S. / Brannigan, J.A.
CitationJournal: J.Biol.Chem. / Year: 2006
Title: Structural and Functional Analysis of a Conjugated Bile Salt Hydrolase from Bifidobacterium longum Reveals an Evolutionary Relationship with Penicillin V Acylase.
Authors: Kumar, R.S. / Brannigan, J.A. / Prabhune, A.A. / Pundle, A.V. / Dodson, G.G. / Dodson, E.J. / Suresh, C.G.
History
DepositionJun 22, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 19, 2006Provider: repository / Type: Initial release
Revision 1.1May 5, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 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)70,3023
Polymers70,2062
Non-polymers961
Water4,089227
1
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)140,6036
Polymers140,4114
Non-polymers1922
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555x-y,-y,-z+1/31
Buried area15770 Å2
ΔGint-149 kcal/mol
Surface area44570 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)125.243, 125.243, 117.028
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
DetailsThe second part of the biological assembly is generated by the two fold axis: -x+1, -y, z+3/2.

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Components

#1: Protein Bile salt hydrolase


Mass: 35102.777 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bifidobacterium longum (bacteria) / Gene: bsh / Plasmid: pET 26b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: Q9KK62, choloylglycine hydrolase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 227 / 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: 3.77 Å3/Da / Density % sol: 67.4 %
Crystal growTemperature: 303 K / Method: vapor diffusion, hanging drop / pH: 6.7
Details: ammonium sulfate 30% w/v, 0.5 M sodium formate, sucrose (1M) 100ml, 40 uL of b-octyl glucosidase (0.50% w/v), pH 6.7, VAPOR DIFFUSION, HANGING DROP, temperature 303K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Nov 8, 2003 / Details: Mirrors
RadiationMonochromator: Osmic mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.49→20 Å / Num. obs: 37135 / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 / Rmerge(I) obs: 0.06
Reflection shellResolution: 2.49→2.55 Å / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3PVA

3pva


Resolution: 2.5→20 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.942 / SU B: 6.727 / SU ML: 0.149 / Cross valid method: THROUGHOUT / ESU R: 0.264 / ESU R Free: 0.211 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.216 1844 5 %RANDOM
Rwork0.17443 ---
obs0.17659 35045 99.65 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 43.015 Å2
Baniso -1Baniso -2Baniso -3
1--0.38 Å2-0.19 Å20 Å2
2---0.38 Å20 Å2
3---0.58 Å2
Refinement stepCycle: LAST / Resolution: 2.5→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4932 0 5 227 5164
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.0215035
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.1841.9226848
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2425626
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.8524.219256
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.62115747
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.8741526
X-RAY DIFFRACTIONr_chiral_restr0.1440.2718
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.023988
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.250.22456
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3240.23455
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1660.2308
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2330.2168
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1540.227
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.2361.53181
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.06524992
X-RAY DIFFRACTIONr_scbond_it3.13832150
X-RAY DIFFRACTIONr_scangle_it4.7024.51856
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.5→2.564 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.299 137 -
Rwork0.248 2519 -
obs--99.59 %

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