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- PDB-2rf8: Crystal Structure of the mutant C2A conjugated bile acid hydrolas... -

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Basic information

Entry
Database: PDB / ID: 2rf8
TitleCrystal Structure of the mutant C2A conjugated bile acid hydrolase from Clostridium perfringens
ComponentsCholoylglycine hydrolase
KeywordsHYDROLASE / Choloylglycine hydrolase / bile salt hydrolase / CBAH / BSH / Ntn-hydrolase
Function / homology
Function and homology information


chenodeoxycholoyltaurine hydrolase activity / choloylglycine hydrolase / choloylglycine hydrolase activity / 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
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: 2.9 Å
AuthorsRossmann, M. / Saenger, W.
CitationJournal: To be Published
Title: Structural basis for the catalytic activity and processing of the conjugated bile salt hydrolase from Clostridium perfringens
Authors: Rossmann, M. / Saenger, W.
History
DepositionSep 28, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 7, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Oct 20, 2021Group: Database references / Derived calculations / Category: database_2 / 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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Choloylglycine hydrolase
B: Choloylglycine hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,6545
Polymers74,3782
Non-polymers2763
Water3,855214
1
A: Choloylglycine hydrolase
B: Choloylglycine hydrolase
hetero molecules

A: Choloylglycine hydrolase
B: Choloylglycine hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)149,30910
Polymers148,7564
Non-polymers5536
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_554y,x,-z-1/41
Buried area20960 Å2
MethodPISA
2
A: Choloylglycine hydrolase
hetero molecules

A: Choloylglycine hydrolase
hetero molecules

B: Choloylglycine hydrolase
hetero molecules

B: Choloylglycine hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)149,30910
Polymers148,7564
Non-polymers5536
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555-x,y,-z1
crystal symmetry operation7_554y,x,-z-1/41
crystal symmetry operation3_555-y,x,z+1/41
Buried area7200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.640, 64.640, 338.833
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number91
Space group name H-MP4122
Components on special symmetry positions
IDModelComponents
11B-367-

HOH

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Components

#1: Protein Choloylglycine hydrolase / Conjugated bile acid hydrolase / CBAH / Bile salt hydrolase


Mass: 37189.059 Da / Num. of mol.: 2 / Mutation: C2A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium perfringens (bacteria) / Gene: cbh / Plasmid: pKLH101 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P54965, choloylglycine hydrolase
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 214 / 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: 2.38 Å3/Da / Density % sol: 48.3 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 10 mM BisTris pH 5.5, 20 mM ammonium sulfate, 25% PEG 3350, vapor diffusion, sitting drop, temperature 291K, Vapor diffusion, sitting drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91841 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: May 4, 2005 / Details: toroidal mirrors
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 2.8→30 Å / Num. obs: 17112 / % possible obs: 90.7 % / Redundancy: 8.3 % / Biso Wilson estimate: 41 Å2 / Rsym value: 0.142 / Net I/σ(I): 12.6
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 8.5 % / Mean I/σ(I) obs: 3.3 / Num. unique all: 1631 / Rsym value: 0.462 / % possible all: 90.3

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Processing

Software
NameVersionClassificationNB
REFMACrefinement
PDB_EXTRACT3data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2bjg

2bjg


Resolution: 2.9→30 Å / Cor.coef. Fo:Fc: 0.916 / Cor.coef. Fo:Fc free: 0.848 / SU B: 17.381 / SU ML: 0.332 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.511 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: Hydrogens have been added in the riding positions
RfactorNum. reflection% reflectionSelection details
Rfree0.275 763 4.9 %RANDOM
Rwork0.206 ---
obs0.209 15424 90.78 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.891 Å2
Baniso -1Baniso -2Baniso -3
1-1.31 Å20 Å20 Å2
2--1.31 Å20 Å2
3----2.61 Å2
Refinement stepCycle: LAST / Resolution: 2.9→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5222 0 18 214 5454
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0225341
X-RAY DIFFRACTIONr_angle_refined_deg0.8861.9537233
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9795655
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.71225.659258
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.35315931
X-RAY DIFFRACTIONr_dihedral_angle_4_deg8.5971516
X-RAY DIFFRACTIONr_chiral_restr0.0610.2811
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.024034
X-RAY DIFFRACTIONr_nbd_refined0.1640.22528
X-RAY DIFFRACTIONr_nbtor_refined0.2960.23675
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1060.2295
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1210.294
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0840.27
X-RAY DIFFRACTIONr_mcbond_it0.2161.53357
X-RAY DIFFRACTIONr_mcangle_it0.37525292
X-RAY DIFFRACTIONr_scbond_it0.24132252
X-RAY DIFFRACTIONr_scangle_it0.3944.51941
LS refinement shellResolution: 2.9→2.975 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.366 60 -
Rwork0.252 1029 -
all-1089 -
obs--89.78 %

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