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- PDB-6g83: Crystal structure of M. tuberculosis DprE1 in complex with sPBTZ1... -

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Basic information

Entry
Database: PDB / ID: 6g83
TitleCrystal structure of M. tuberculosis DprE1 in complex with sPBTZ169 (sulfonylPBTZ)
ComponentsDecaprenylphosphoryl-beta-D-ribose oxidase
KeywordsOXIDOREDUCTASE / DprE1 / M. tuberculosis / inhibitor / complex / BTZ
Function / homology
Function and homology information


arabinan biosynthetic process / cell wall polysaccharide biosynthetic process / decaprenylphospho-beta-D-ribofuranose 2-dehydrogenase / D-arabinono-1,4-lactone oxidase activity / capsule polysaccharide biosynthetic process / FAD binding / cell wall organization / periplasmic space / oxidoreductase activity / response to antibiotic ...arabinan biosynthetic process / cell wall polysaccharide biosynthetic process / decaprenylphospho-beta-D-ribofuranose 2-dehydrogenase / D-arabinono-1,4-lactone oxidase activity / capsule polysaccharide biosynthetic process / FAD binding / cell wall organization / periplasmic space / oxidoreductase activity / response to antibiotic / membrane / plasma membrane
Similarity search - Function
D-arabinono-1,4-lactone oxidase, C-terminal domain / D-arabinono-1,4-lactone oxidase / FAD linked oxidase, N-terminal / FAD binding domain / FAD-binding domain, PCMH-type / PCMH-type FAD-binding domain profile. / FAD-binding, type PCMH, subdomain 2 / FAD-binding, type PCMH-like superfamily
Similarity search - Domain/homology
Chem-EQ8 / FLAVIN-ADENINE DINUCLEOTIDE / Decaprenylphosphoryl-beta-D-ribose oxidase / Decaprenylphosphoryl-beta-D-ribose oxidase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsPiton, J. / Makarov, V. / Cole, S.T.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
European Union260872 Switzerland
CitationJournal: Antimicrob. Agents Chemother. / Year: 2018
Title: Structure-Based Drug Design and Characterization of Sulfonyl-Piperazine Benzothiazinone Inhibitors of DprE1 from Mycobacterium tuberculosis.
Authors: Piton, J. / Vocat, A. / Lupien, A. / Foo, C.S. / Riabova, O. / Makarov, V. / Cole, S.T.
History
DepositionApr 7, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 1, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 3, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.title / _citation_author.name
Revision 1.2Mar 8, 2023Group: Database references / Source and taxonomy
Category: database_2 / entity_src_gen ...database_2 / entity_src_gen / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_src_gen.gene_src_strain / _entity_src_gen.pdbx_gene_src_gene / _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name / _struct_ref.db_code / _struct_ref.pdbx_db_accession / _struct_ref_seq.pdbx_db_accession / _struct_ref_seq_dif.pdbx_seq_db_accession_code
Revision 1.3Feb 7, 2024Group: 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: Decaprenylphosphoryl-beta-D-ribose oxidase
B: Decaprenylphosphoryl-beta-D-ribose oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,3376
Polymers104,7832
Non-polymers2,5544
Water1,946108
1
A: Decaprenylphosphoryl-beta-D-ribose oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,6683
Polymers52,3911
Non-polymers1,2772
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Decaprenylphosphoryl-beta-D-ribose oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,6683
Polymers52,3911
Non-polymers1,2772
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)78.164, 84.024, 81.666
Angle α, β, γ (deg.)90.00, 103.98, 90.00
Int Tables number4
Space group name H-MP1211
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein Decaprenylphosphoryl-beta-D-ribose oxidase / Decaprenylphospho-beta-D-ribofuranose 2-dehydrogenase / Decaprenylphosphoryl-beta-D-ribofuranose 2'- ...Decaprenylphospho-beta-D-ribofuranose 2-dehydrogenase / Decaprenylphosphoryl-beta-D-ribofuranose 2'-epimerase subunit DprE1 / Decaprenyl-phosphoribose 2'-epimerase subunit 1 / Decaprenylphosphoryl-beta-D-ribofuranose 2'-oxidase / Decaprenylphosphoryl-beta-D-ribose 2-epimerase flavoprotein subunit / FAD-dependent decaprenylphosphoryl-beta-D-ribofuranose 2-oxidase


Mass: 52391.332 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria)
Gene: dprE1, Rv3790 / Production host: Escherichia coli (E. coli)
References: UniProt: P9WJF1, UniProt: P9WJF0*PLUS, decaprenylphospho-beta-D-ribofuranose 2-dehydrogenase
#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE / Flavin adenine dinucleotide


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Chemical ChemComp-EQ8 / [2-(4-cyclohexylsulfonylpiperazin-1-yl)-4-oxidanylidene-6-(trifluoromethyl)-1,3-benzothiazin-8-yl]-oxidanylidene-azanium


Mass: 491.528 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C19H22F3N4O4S2 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 108 / 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: 2.85 Å3/Da / Density % sol: 56.84 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: containing 100 mM imidazole, pH 7.2-7.5, 18-24 % polypropyleneglycol 400

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Jan 22, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→49.18 Å / Num. obs: 79124 / % possible obs: 98.81 % / Redundancy: 2 % / Biso Wilson estimate: 47.7 Å2 / Net I/σ(I): 16.42
Reflection shellResolution: 2.4→2.486 Å

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4NCR

4ncr


Resolution: 2.4→49.179 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.55
RfactorNum. reflection% reflection
Rfree0.2257 1750 4.4 %
Rwork0.1979 --
obs0.1991 39780 98.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.4→49.179 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6234 0 170 108 6512
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0086557
X-RAY DIFFRACTIONf_angle_d0.9458954
X-RAY DIFFRACTIONf_dihedral_angle_d15.7612275
X-RAY DIFFRACTIONf_chiral_restr0.0511005
X-RAY DIFFRACTIONf_plane_restr0.0061143
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.46490.31141350.28712864X-RAY DIFFRACTION98
2.4649-2.53740.27661370.27372902X-RAY DIFFRACTION98
2.5374-2.61930.29991270.25282879X-RAY DIFFRACTION98
2.6193-2.71290.27921420.24582906X-RAY DIFFRACTION99
2.7129-2.82150.25111260.23342917X-RAY DIFFRACTION99
2.8215-2.94990.25781370.23782894X-RAY DIFFRACTION99
2.9499-3.10540.23361350.20952928X-RAY DIFFRACTION99
3.1054-3.30.24011320.2132925X-RAY DIFFRACTION99
3.3-3.55470.241390.2072941X-RAY DIFFRACTION99
3.5547-3.91230.19221370.18292931X-RAY DIFFRACTION99
3.9123-4.47810.21241340.1672956X-RAY DIFFRACTION99
4.4781-5.64060.18451380.16642964X-RAY DIFFRACTION100
5.6406-49.18940.22221310.1893023X-RAY DIFFRACTION99

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