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- PDB-4wl3: Crystal structure determination of Bile Salt Hydrolase from Enter... -

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Basic information

Entry
Database: PDB / ID: 4wl3
TitleCrystal structure determination of Bile Salt Hydrolase from Enterococcus feacalis
ComponentsBile salt hydrolase
KeywordsHYDROLASE / Ntn-Hydrolase / E. faecalis Bile Salt Hydrolase / Cytosolic
Function / homology
Function and homology information


: / 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
Biological speciesEnterococcus faecalis T2 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.01 Å
AuthorsRamasamy, S. / Chand, D. / Suresh, C.G.
Funding support India, 1items
OrganizationGrant numberCountry
DSTBSC0119 India
CitationJournal: To Be Published
Title: Crystal structure determination of Bile Salt Hydrolase from Enterococcus feacalis
Authors: Chand, D. / Suresh, C.G. / Ramasamy, S.
History
DepositionOct 6, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 11, 2015Provider: repository / Type: Initial release
Revision 1.1Apr 20, 2016Group: Other
Revision 1.2Nov 8, 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 / pdbx_struct_oper_list / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation / _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

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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
C: Bile salt hydrolase
D: Bile salt hydrolase


Theoretical massNumber of molelcules
Total (without water)151,6254
Polymers151,6254
Non-polymers00
Water2,144119
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18910 Å2
ΔGint-81 kcal/mol
Surface area45300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.200, 131.620, 86.720
Angle α, β, γ (deg.)90.00, 94.48, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: CYS / Beg label comp-ID: CYS / End auth comp-ID: ASN / End label comp-ID: ASN / Refine code: _ / Auth seq-ID: 2 - 324 / Label seq-ID: 1 - 323

Dom-IDEns-IDAuth asym-IDLabel asym-ID
11AA
21BB
12AA
22CC
13AA
23DD
14BB
24CC
15BB
25DD
16CC
26DD

NCS ensembles :
ID
1
2
3
4
5
6

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Components

#1: Protein
Bile salt hydrolase


Mass: 37906.273 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterococcus faecalis T2 (bacteria) / Strain: T2 / Gene: EFBG_01849 / Plasmid: pET22b+ / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: C7CXJ5, choloylglycine hydrolase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 119 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.54 Å3/Da / Density % sol: 51.7 % / Description: Monoclinic
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 2M Ammonium Sulfate, 5% Isopropanol / PH range: 5.0- 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: RRCAT INDUS-2 / Beamline: PX-BL21 / Wavelength: 0.979 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Jan 17, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.01→41.07 Å / Num. obs: 97208 / % possible obs: 99.3 % / Redundancy: 2.6 % / Rmerge(I) obs: 0.084 / Net I/σ(I): 9
Reflection shellResolution: 2.01→2.01 Å / Redundancy: 2.5 % / Mean I/σ(I) obs: 3.5 / % possible all: 97.8

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Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
Aimlessdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2RLC

2rlc


Resolution: 2.01→41.07 Å / Cor.coef. Fo:Fc: 0.924 / Cor.coef. Fo:Fc free: 0.907 / SU B: 3.794 / SU ML: 0.107 / Cross valid method: THROUGHOUT / ESU R: 0.202 / ESU R Free: 0.168 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23463 4645 5 %RANDOM
Rwork0.20506 ---
obs0.20653 88714 95.34 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.784 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å2-0 Å20 Å2
2--0.01 Å20 Å2
3----0.02 Å2
Refinement stepCycle: LAST / Resolution: 2.01→41.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10388 0 0 119 10507
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.01910624
X-RAY DIFFRACTIONr_bond_other_d0.0090.029760
X-RAY DIFFRACTIONr_angle_refined_deg1.8211.95314404
X-RAY DIFFRACTIONr_angle_other_deg1.529322492
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.31851288
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.97425.037540
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.367151788
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.1931540
X-RAY DIFFRACTIONr_chiral_restr0.1140.21564
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0212208
X-RAY DIFFRACTIONr_gen_planes_other0.0070.022528
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_it1.9091.715164
X-RAY DIFFRACTIONr_mcbond_other1.9081.715163
X-RAY DIFFRACTIONr_mcangle_it2.932.5556448
X-RAY DIFFRACTIONr_mcangle_other2.9292.5566449
X-RAY DIFFRACTIONr_scbond_it2.5522.0095460
X-RAY DIFFRACTIONr_scbond_other2.5522.0095461
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.9462.9057957
X-RAY DIFFRACTIONr_long_range_B_refined5.46314.13811821
X-RAY DIFFRACTIONr_long_range_B_other5.45914.13811803
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A192000.1
12B192000.1
21A189790.11
22C189790.11
31A189810.11
32D189810.11
41B192210.11
42C192210.11
51B194090.1
52D194090.1
61C190350.11
62D190350.11
LS refinement shellResolution: 2.012→2.064 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.266 281 -
Rwork0.232 6036 -
obs--87.94 %

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