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

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Basic information

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


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
Bile salt hydrolase/transferase
Similarity search - Component
Biological speciesCLOSTRIDIUM PERFRINGENS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 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 1.0May 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_ncs_dom_lim / struct_site
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 / _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

Downloads & links

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Assembly

Deposited unit
A: CHOLOYLGLYCINE HYDROLASE
B: CHOLOYLGLYCINE HYDROLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,5664
Polymers74,4422
Non-polymers1242
Water7,260403
1
A: CHOLOYLGLYCINE HYDROLASE
B: CHOLOYLGLYCINE HYDROLASE
hetero molecules

A: CHOLOYLGLYCINE HYDROLASE
B: CHOLOYLGLYCINE HYDROLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)149,1338
Polymers148,8854
Non-polymers2484
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_554y,x,-z-1/41
MethodPQS
Unit cell
Length a, b, c (Å)63.784, 63.784, 341.367
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number91
Space group name H-MP4122
Components on special symmetry positions
IDModelComponents
11B-2039-

HOH

21B-2188-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: CYS / Beg label comp-ID: CYS / End auth comp-ID: ASN / End label comp-ID: ASN / Refine code: 1 / Auth seq-ID: 2 - 320 / Label seq-ID: 2 - 320

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

NCS oper: (Code: given
Matrix: (-0.997, -0.003, -0.078), (-0.002, -0.998, 0.068), (-0.078, 0.068, 0.995)
Vector: 62.5946, 68.85458, 0.08593)

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Components

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


Mass: 37221.125 Da / Num. of mol.: 2
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-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 403 / 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: 47 %
Crystal growpH: 5.5
Details: 25% PEG4000, 200 MM AMMONIUMSULFATE, 100 MM BISTRIS PH 5.5

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.9797
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Aug 19, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9797 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 34729 / % possible obs: 81 % / Observed criterion σ(I): 3 / Redundancy: 5.6 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 19
Reflection shellResolution: 2.1→2.18 Å / Rmerge(I) obs: 0.16 / Mean I/σ(I) obs: 8.4 / % possible all: 84

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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 2BJF

2bjf


Resolution: 2.1→50 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.926 / SU B: 5.07 / SU ML: 0.135 / Cross valid method: THROUGHOUT / ESU R: 0.338 / ESU R Free: 0.233 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.246 1732 5 %RANDOM
Rwork0.2 ---
obs0.203 32880 81.1 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 30.25 Å2
Baniso -1Baniso -2Baniso -3
1-1.75 Å20 Å20 Å2
2--1.75 Å20 Å2
3----3.5 Å2
Refinement stepCycle: LAST / Resolution: 2.1→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5216 0 8 403 5627
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0225326
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.0541.9517214
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7095654
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.52925.659258
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.97315930
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.9791516
X-RAY DIFFRACTIONr_chiral_restr0.0780.2810
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.024030
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1760.22292
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2960.23669
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1110.2394
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.30.291
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1250.217
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.4421.53375
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.76425286
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.81732243
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it1.2584.51928
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
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 2536 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
tight positional0.030.05
tight thermal0.190.5
LS refinement shellResolution: 2.1→2.15 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.305 134
Rwork0.228 2450

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