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- PDB-6a8q: R207A mutant of highly active EfBSH -

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Basic information

Entry
Database: PDB / ID: 6a8q
TitleR207A mutant of highly active EfBSH
ComponentsBile salt hydrolase
KeywordsHYDROLASE / Ntn / Bile Salt Hydrolase / Gut Microbiome
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 Å
AuthorsRamasamy, S. / Yadav, Y.
Funding support India, 1items
OrganizationGrant numberCountry
Council of Scientific & Industrial Research India
CitationJournal: To Be Published
Title: R207A mutant of highly active EfBSH
Authors: Ramasamy, S. / Yadav, Y.
History
DepositionJul 10, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 10, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 25, 2019Group: Data collection / Category: reflns_shell
Item: _reflns_shell.Rmerge_I_obs / _reflns_shell.pdbx_Rpim_I_all / _reflns_shell.pdbx_Rrim_I_all
Revision 1.2Nov 22, 2023Group: Data collection / Database references / 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
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

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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)151,2814
Polymers151,2814
Non-polymers00
Water6,792377
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, Tetramer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18460 Å2
ΔGint-86 kcal/mol
Surface area45420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.330, 156.450, 72.910
Angle α, β, γ (deg.)90.00, 98.62, 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: 0 / Beg auth comp-ID: CYS / Beg label comp-ID: CYS / End auth comp-ID: ASN / End label comp-ID: ASN / Refine code: 0 / 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: 37820.156 Da / Num. of mol.: 4 / Mutation: R207A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterococcus faecalis T2 (bacteria) / Gene: EFBG_01849
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: C7CXJ5
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 377 / 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: 2.21 Å3/Da / Density % sol: 44.38 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.1 M Sodium Citrate Tribasic Dihydrate, 22 % PEG 1000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: RRCAT INDUS-2 / Beamline: PX-BL21 / Wavelength: 0.97949 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: May 4, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 1.84→39.11 Å / Num. obs: 83294 / % possible obs: 98.7 % / Redundancy: 4 % / CC1/2: 0.978 / Rmerge(I) obs: 0.196 / Rpim(I) all: 0.11 / Rrim(I) all: 0.225 / Net I/σ(I): 5
Reflection shellResolution: 2→2 Å / Mean I/σ(I) obs: 2 / Num. unique obs: 4365 / CC1/2: 0.992

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Processing

Software
NameVersionClassification
REFMAC5.8.0222refinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4WL3

4wl3


Resolution: 2→39.01 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.904 / Cross valid method: THROUGHOUT / ESU R: 0.229 / ESU R Free: 0.178 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23215 4095 4.9 %RANDOM
Rwork0.20138 ---
obs0.20288 79140 94.12 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 15.915 Å2
Baniso -1Baniso -2Baniso -3
1-1.14 Å20 Å2-2.24 Å2
2---1.1 Å20 Å2
3---0.61 Å2
Refinement stepCycle: 1 / Resolution: 2→39.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10364 0 0 377 10741
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.01510643
X-RAY DIFFRACTIONr_bond_other_d0.0010.0179308
X-RAY DIFFRACTIONr_angle_refined_deg1.4751.7414442
X-RAY DIFFRACTIONr_angle_other_deg3.6221.73521830
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.24851304
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.12523.098481
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.831151607
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.6721536
X-RAY DIFFRACTIONr_chiral_restr0.0720.21372
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0212016
X-RAY DIFFRACTIONr_gen_planes_other0.0110.022084
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_it1.4151.4965180
X-RAY DIFFRACTIONr_mcbond_other1.4151.4965181
X-RAY DIFFRACTIONr_mcangle_it2.2752.2386472
X-RAY DIFFRACTIONr_mcangle_other2.2752.2386473
X-RAY DIFFRACTIONr_scbond_it2.1311.745463
X-RAY DIFFRACTIONr_scbond_other2.1311.745462
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.3622.5157963
X-RAY DIFFRACTIONr_long_range_B_refined4.51717.57511628
X-RAY DIFFRACTIONr_long_range_B_other4.51417.55611579
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)
11A105020.1
12B105020.1
21A104990.09
22C104990.09
31A105290.09
32D105290.09
41B105740.09
42C105740.09
51B105610.09
52D105610.09
61C106110.08
62D106110.08
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.301 295 -
Rwork0.263 5556 -
obs--89.48 %

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