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- PDB-2bjf: Crystal Structure of Conjugated Bile Acid Hydrolase from Clostrid... -

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Basic information

Entry
Database: PDB / ID: 2bjf
TitleCrystal Structure of Conjugated Bile Acid Hydrolase from Clostridium perfringens in Complex with Reaction Products Taurine and Deoxycholate
ComponentsCHOLOYLGLYCINE HYDROLASE
KeywordsHYDROLASE / AMIDOHYDROLASE / NTN-HYDROLASE / BILE ACIDS / BSH
Function / homology
Function and homology information


L-phenylalanine conjugated cholate hydrolase activity / L-arginine conjugated cholate hydrolase activity / L-histidine conjugated cholate hydrolase activity / 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 / 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
2-AMINOETHANESULFONIC ACID / Bile salt hydrolase/transferase
Similarity search - Component
Biological speciesCLOSTRIDIUM PERFRINGENS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.67 Å
AuthorsRossocha, M. / Schultz-Heienbrok, R. / Von Moeller, H. / Coleman, J.P. / Saenger, W.
CitationJournal: Biochemistry / Year: 2005
Title: Conjugated Bile Acid Hydrolase is a Tetrameric N-Terminal Thiol Hydrolase with Specific Recognition of its Cholyl But not of its Tauryl Product
Authors: Rossocha, M. / Schultz-Heienbrok, R. / Von Moeller, H. / Coleman, J.P. / Saenger, W.
History
DepositionFeb 2, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 3, 2005Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CHOLOYLGLYCINE HYDROLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,9235
Polymers37,2211
Non-polymers7024
Water5,621312
1
A: CHOLOYLGLYCINE HYDROLASE
hetero molecules

A: CHOLOYLGLYCINE HYDROLASE
hetero molecules

A: CHOLOYLGLYCINE HYDROLASE
hetero molecules

A: CHOLOYLGLYCINE HYDROLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)151,69220
Polymers148,8854
Non-polymers2,80816
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555x,-y+1/2,-z+1/21
crystal symmetry operation11_555-x+1/2,y,-z+1/21
crystal symmetry operation14_555-x+1/2,-y+1/2,z1
MethodPQS
Unit cell
Length a, b, c (Å)88.848, 90.835, 188.547
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number22
Space group name H-MF222
Components on special symmetry positions
IDModelComponents
11A-2073-

HOH

21A-2100-

HOH

31A-2199-

HOH

41A-2221-

HOH

51A-2266-

HOH

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Components

#1: Protein CHOLOYLGLYCINE HYDROLASE / CONJUGATED BILE ACID HYDROLASE / CBAH / BILE SALT HYDROLASE


Mass: 37221.125 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) CLOSTRIDIUM PERFRINGENS (bacteria) / Plasmid: PKK233-2 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P54965, choloylglycine hydrolase
#2: Chemical ChemComp-DXC / (3ALPHA,5BETA,12ALPHA)-3,12-DIHYDROXYCHOLAN-24-OIC ACID / DEOXYCHOLIC ACID


Mass: 392.572 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H40O4 / Comment: detergent*YM
#3: Chemical ChemComp-TAU / 2-AMINOETHANESULFONIC ACID


Mass: 125.147 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H7NO3S
#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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 312 / 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: 2.6 Å3/Da / Density % sol: 51 %
Crystal growpH: 6 / Details: 2.6M AMMONIUM SULFATE, 100 MM NACITRATE PH 6.0

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.9766
DetectorType: MARRESEARCH / Date: Oct 15, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9766 Å / Relative weight: 1
ReflectionResolution: 1.67→50 Å / Num. obs: 42911 / % possible obs: 97 % / Observed criterion σ(I): 3 / Redundancy: 3.6 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 29.4
Reflection shellResolution: 1.67→1.73 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.11 / Mean I/σ(I) obs: 8 / % possible all: 97

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3PVA

3pva


Resolution: 1.67→94.07 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.94 / SU B: 1.682 / SU ML: 0.059 / Cross valid method: THROUGHOUT / ESU R: 0.102 / ESU R Free: 0.094 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.201 2166 5 %RANDOM
Rwork0.182 ---
obs0.183 40736 97.1 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 14.71 Å2
Baniso -1Baniso -2Baniso -3
1-1.44 Å20 Å20 Å2
2---0.79 Å20 Å2
3----0.64 Å2
Refinement stepCycle: LAST / Resolution: 1.67→94.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2608 0 47 312 2967
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0222783
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.031.9663788
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2615343
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.42625.912137
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.3415477
X-RAY DIFFRACTIONr_dihedral_angle_4_deg8.86158
X-RAY DIFFRACTIONr_chiral_restr0.0670.2426
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.022115
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1660.21249
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3010.21948
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.0660.2272
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1440.2136
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0580.237
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.4151.51738
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.50122731
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.66631191
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it1.0254.51057
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.67→1.71 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.232 146
Rwork0.206 2976

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