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- PDB-6hf3: M tuberculosis DprE1 in complex with a covalently bound nitrobenz... -

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Basic information

Entry
Database: PDB / ID: 6hf3
TitleM tuberculosis DprE1 in complex with a covalently bound nitrobenzothiazinone
ComponentsDecaprenylphosphoryl-beta-D-ribose oxidase
KeywordsFLAVOPROTEIN / oxidation-reduction process / isomerase / arabinan biosynthetic process
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 / plasma membrane
Similarity search - Function
D-arabinono-1,4-lactone oxidase, C-terminal domain / D-arabinono-1,4-lactone oxidase / L-gulonolactone/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-26J / FLAVIN-ADENINE DINUCLEOTIDE / Decaprenylphosphoryl-beta-D-ribose oxidase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsFutterer, K. / Batt, S.M. / Besra, G.S.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Medical Research Council (United Kingdom)MR/K012118/1 United Kingdom
CitationJournal: Sci Rep / Year: 2018
Title: Novel insight into the reaction of nitro, nitroso and hydroxylamino benzothiazinones and of benzoxacinones with Mycobacterium tuberculosis DprE1.
Authors: Richter, A. / Rudolph, I. / Mollmann, U. / Voigt, K. / Chung, C.W. / Singh, O.M.P. / Rees, M. / Mendoza-Losana, A. / Bates, R. / Ballell, L. / Batt, S. / Veerapen, N. / Futterer, K. / Besra, ...Authors: Richter, A. / Rudolph, I. / Mollmann, U. / Voigt, K. / Chung, C.W. / Singh, O.M.P. / Rees, M. / Mendoza-Losana, A. / Bates, R. / Ballell, L. / Batt, S. / Veerapen, N. / Futterer, K. / Besra, G. / Imming, P. / Argyrou, A.
History
DepositionAug 21, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 29, 2018Provider: repository / Type: Initial release
Revision 1.1Sep 19, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Jan 17, 2024Group: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)107,2396
Polymers104,7832
Non-polymers2,4564
Water1,09961
1
A: Decaprenylphosphoryl-beta-D-ribose oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,6193
Polymers52,3911
Non-polymers1,2282
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Decaprenylphosphoryl-beta-D-ribose oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,6193
Polymers52,3911
Non-polymers1,2282
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)78.230, 84.110, 80.770
Angle α, β, γ (deg.)90.00, 103.36, 90.00
Int Tables number4
Space group name H-MP1211

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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 (bacteria) / Gene: dprE1, Rv3790 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P9WJF1, decaprenylphospho-beta-D-ribofuranose 2-dehydrogenase
#2: Chemical ChemComp-26J / 2-(4-(cyclohexylmethyl)piperazin-1-yl)-8-nitro-6-(trifluoromethyl)-4H-benzo[e][1,3]thiazin-4-one, bound form


Mass: 442.498 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H25F3N4O2S
#3: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 61 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.47 Å3/Da / Density % sol: 50.26 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.4
Details: 24 - 34 % w/v polypropylene glcyol 400, 100 mM imidazole

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97631 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: May 19, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97631 Å / Relative weight: 1
ReflectionResolution: 2.2→84.1 Å / Num. obs: 51086 / % possible obs: 98.6 % / Observed criterion σ(F): 0 / Redundancy: 3.8 % / Rmerge(I) obs: 0.039 / Net I/σ(I): 14.7
Reflection shellResolution: 2.2→2.26 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.61 / Mean I/σ(I) obs: 2.4 / % possible all: 97

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Processing

Software
NameVersionClassification
PHENIX1.7.3_928refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4FDP

4fdp


Resolution: 2.2→76.113 Å / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 0.71 / Phase error: 29.75 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2378 2590 5.07 %
Rwork0.2063 --
obs0.2079 51061 98.48 %
Solvent computationShrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 38.028 Å2 / ksol: 0.312 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-4.219 Å20 Å2-16.5602 Å2
2--7.3009 Å20 Å2
3----11.5199 Å2
Refinement stepCycle: LAST / Resolution: 2.2→76.113 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6357 0 144 61 6562
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0086653
X-RAY DIFFRACTIONf_angle_d1.1789077
X-RAY DIFFRACTIONf_dihedral_angle_d14.3182343
X-RAY DIFFRACTIONf_chiral_restr0.0831020
X-RAY DIFFRACTIONf_plane_restr0.0051154
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.240.37121390.32832506X-RAY DIFFRACTION97
2.24-2.28310.3921350.30442474X-RAY DIFFRACTION98
2.2831-2.32970.35031110.28952571X-RAY DIFFRACTION98
2.3297-2.38040.34961260.2782562X-RAY DIFFRACTION98
2.3804-2.43580.35381280.26412505X-RAY DIFFRACTION97
2.4358-2.49670.28761310.25892501X-RAY DIFFRACTION97
2.4967-2.56420.2961580.26472507X-RAY DIFFRACTION99
2.5642-2.63960.32031510.25012522X-RAY DIFFRACTION98
2.6396-2.72480.30651210.24992555X-RAY DIFFRACTION99
2.7248-2.82220.26481300.24432573X-RAY DIFFRACTION99
2.8222-2.93520.31971560.24962518X-RAY DIFFRACTION99
2.9352-3.06880.26331470.24652549X-RAY DIFFRACTION99
3.0688-3.23060.28581340.23592564X-RAY DIFFRACTION99
3.2306-3.4330.26991220.23142576X-RAY DIFFRACTION99
3.433-3.69810.2521550.21162566X-RAY DIFFRACTION99
3.6981-4.07020.19211410.1882577X-RAY DIFFRACTION99
4.0702-4.65910.16141470.15492597X-RAY DIFFRACTION100
4.6591-5.86970.17781290.16342596X-RAY DIFFRACTION99
5.8697-76.15840.22651290.17842652X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.7803-0.34441.26731.2892-0.06322.2530.0426-0.1875-0.0970.08740.0823-0.0040.1088-0.08730.01830.2686-0.01490.04670.2423-0.00670.313612.5474-11.172736.5603
22.63210.95341.1711.51450.18762.04390.11440.4214-0.2479-0.02490.187-0.00060.37410.170.02160.41770.03240.00150.36060.00890.4097-21.6161-17.7310.6873
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resseq 7:461)
2X-RAY DIFFRACTION2(chain B and resseq 7:461)

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