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- PDB-7br2: BT4096 a gut microbial diltiazem-metabolizing enzyme -

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Basic information

Entry
Database: PDB / ID: 7br2
TitleBT4096 a gut microbial diltiazem-metabolizing enzyme
ComponentsLipolytic enzyme, G-D-S-L family
KeywordsHYDROLASE / gut microbe / diltiazem / drug metabolism / SGNH / GDSL / serine esterase
Function / homologySGNH hydrolase-type esterase domain / GDSL-like Lipase/Acylhydrolase family / SGNH hydrolase superfamily / Lipolytic enzyme, G-D-S-L family
Function and homology information
Biological speciesBacteroides thetaiotaomicron (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.33 Å
AuthorsKo, T.-P. / Chen, C.-C. / Guo, R.-T.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2020
Title: Structure of a gut microbial diltiazem-metabolizing enzyme suggests possible substrate binding mode.
Authors: Zhou, S. / Ko, T.P. / Huang, J.W. / Liu, W. / Zheng, Y. / Wu, S. / Wang, Q. / Xie, Z. / Liu, Z. / Chen, C.C. / Guo, R.T.
History
DepositionMar 26, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 6, 2020Provider: repository / Type: Initial release
Revision 1.1Jun 3, 2020Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jun 17, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Mar 27, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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: Lipolytic enzyme, G-D-S-L family
B: Lipolytic enzyme, G-D-S-L family
C: Lipolytic enzyme, G-D-S-L family
D: Lipolytic enzyme, G-D-S-L family


Theoretical massNumber of molelcules
Total (without water)206,8594
Polymers206,8594
Non-polymers00
Water18,5911032
1
A: Lipolytic enzyme, G-D-S-L family


Theoretical massNumber of molelcules
Total (without water)51,7151
Polymers51,7151
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Lipolytic enzyme, G-D-S-L family


Theoretical massNumber of molelcules
Total (without water)51,7151
Polymers51,7151
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Lipolytic enzyme, G-D-S-L family


Theoretical massNumber of molelcules
Total (without water)51,7151
Polymers51,7151
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Lipolytic enzyme, G-D-S-L family


Theoretical massNumber of molelcules
Total (without water)51,7151
Polymers51,7151
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)86.693, 133.797, 182.322
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
41

NCS domain segments:

Ens-ID: 1 / Beg auth comp-ID: GLY / Beg label comp-ID: GLY / End auth comp-ID: ILE / End label comp-ID: ILE / Auth seq-ID: -1 - 440 / Label seq-ID: 9 - 450

Dom-IDComponent-IDSelection detailsAuth asym-IDLabel asym-ID
11(chain 'A' and resid -1 through 440)AA
22(chain 'B' and resid -1 through 440)BB
33chain 'C'CC
44(chain 'D' and resid -1 through 440)DD

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Components

#1: Protein
Lipolytic enzyme, G-D-S-L family


Mass: 51714.852 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides thetaiotaomicron (bacteria)
Gene: BT_4096 / Plasmid: pET32a
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q8A0C5
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1032 / 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: 2.56 Å3/Da / Density % sol: 51.87 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: protein: 10 mg/mL in 20 mM Tris, 500 mM NaCl, 10 mM DTT, pH 8.5 reservoir: 20% PEG 6000, 0.25 M Na-citrate, pH 5.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: TPS 05A / Wavelength: 1 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Jan 17, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.33→25 Å / Num. obs: 91059 / % possible obs: 99.8 % / Redundancy: 7.5 % / Biso Wilson estimate: 33.59 Å2 / CC1/2: 0.936 / Rmerge(I) obs: 0.101 / Rpim(I) all: 0.039 / Net I/σ(I): 25.06
Reflection shellResolution: 2.33→2.41 Å / Redundancy: 7.4 % / Rmerge(I) obs: 0.667 / Mean I/σ(I) obs: 3.6 / Num. unique obs: 8956 / CC1/2: 0.856 / Rpim(I) all: 0.257 / % possible all: 99.3

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
HKL-2000data processing
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 2.33→24.94 Å / SU ML: 0.2566 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 23.6236
RfactorNum. reflection% reflection
Rfree0.2215 1999 2.2 %
Rwork0.1821 --
obs0.183 90969 99.63 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 40.02 Å2
Refinement stepCycle: LAST / Resolution: 2.33→24.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14429 0 0 1032 15461
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007314733
X-RAY DIFFRACTIONf_angle_d0.971119815
X-RAY DIFFRACTIONf_chiral_restr0.0562053
X-RAY DIFFRACTIONf_plane_restr0.00612585
X-RAY DIFFRACTIONf_dihedral_angle_d16.59068907
LS refinement shellResolution: 2.33→2.39 Å
RfactorNum. reflection% reflection
Rfree0.2658 138 -
Rwork0.2342 6106 -
obs--97.55 %

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