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- PDB-6hf0: M. tuberculosis DprE1 covalently bound to a nitrobenzoxacinone. -

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Basic information

Entry
Database: PDB / ID: 6hf0
TitleM. tuberculosis DprE1 covalently bound to a nitrobenzoxacinone.
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 / : / 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
FLAVIN-ADENINE DINUCLEOTIDE / Chem-G1H / Decaprenylphosphoryl-beta-D-ribose oxidase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.384 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)107,0966
Polymers104,7832
Non-polymers2,3144
Water1,31573
1
A: Decaprenylphosphoryl-beta-D-ribose oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,5483
Polymers52,3911
Non-polymers1,1572
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Decaprenylphosphoryl-beta-D-ribose oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,5483
Polymers52,3911
Non-polymers1,1572
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)78.640, 85.410, 80.410
Angle α, β, γ (deg.)90.00, 103.20, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
12
22
13
23
14
24

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111chain a and resi 7:260
211chain b and resi 7:260
112chain a and resi 303:313
212chain b and resi 303:313
113chain a and resi 331:461
213chain b and resi 331:461
114chain a and resi 900
214chain b and resi 900

NCS ensembles :
ID
1
2
3
4

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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-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Chemical ChemComp-G1H / 2-[(2~{S},6~{R})-2,6-dimethylpiperidin-1-yl]-8-nitro-6-(trifluoromethyl)-1,3-benzoxazin-4-one


Mass: 371.311 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H16F3N3O4 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 73 / 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: 2.51 Å3/Da / Density % sol: 50.98 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.4
Details: 24 - 34 % w/v polypropylene glycol, 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 PILATUS 2M / Detector: PIXEL / Date: Feb 2, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97631 Å / Relative weight: 1
ReflectionResolution: 2.38→78.3 Å / Num. obs: 40283 / % possible obs: 97.1 % / Observed criterion σ(F): 0 / Redundancy: 5.3 % / Rmerge(I) obs: 0.048 / Net I/σ(I): 16.3
Reflection shellResolution: 2.38→2.45 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.513 / Mean I/σ(I) obs: 2.1 / % possible all: 80.7

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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: 2.384→78.285 Å / SU ML: 0.41 / Cross valid method: FREE R-VALUE / σ(F): 1.53 / Phase error: 32.51
RfactorNum. reflection% reflection
Rfree0.2411 2016 5.01 %
Rwork0.2119 --
obs0.2134 40251 97.01 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Bsol: 43.059 Å2 / ksol: 0.315 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-9.9032 Å20 Å2-19.2396 Å2
2--6.4865 Å20 Å2
3----16.3897 Å2
Refinement stepCycle: LAST / Resolution: 2.384→78.285 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6290 0 148 73 6511
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0086591
X-RAY DIFFRACTIONf_angle_d1.1828992
X-RAY DIFFRACTIONf_dihedral_angle_d14.5952305
X-RAY DIFFRACTIONf_chiral_restr0.0771014
X-RAY DIFFRACTIONf_plane_restr0.0061144
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A1813X-RAY DIFFRACTIONPOSITIONAL
12B1813X-RAY DIFFRACTIONPOSITIONAL0.042
21A95X-RAY DIFFRACTIONPOSITIONAL
22B95X-RAY DIFFRACTIONPOSITIONAL0.028
31A1037X-RAY DIFFRACTIONPOSITIONAL
32B1037X-RAY DIFFRACTIONPOSITIONAL0.061
41A53X-RAY DIFFRACTIONPOSITIONAL
42B53X-RAY DIFFRACTIONPOSITIONAL0.045
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.384-2.44360.3862960.34522293X-RAY DIFFRACTION81
2.4436-2.50970.39611410.31392452X-RAY DIFFRACTION88
2.5097-2.58350.36351580.29222710X-RAY DIFFRACTION98
2.5835-2.66690.3531360.27752773X-RAY DIFFRACTION98
2.6669-2.76220.3561510.2732739X-RAY DIFFRACTION99
2.7622-2.87280.31841510.26492757X-RAY DIFFRACTION99
2.8728-3.00360.32341420.26022791X-RAY DIFFRACTION99
3.0036-3.1620.30861500.25262794X-RAY DIFFRACTION99
3.162-3.36010.31451460.26782783X-RAY DIFFRACTION99
3.3601-3.61950.30721320.25442811X-RAY DIFFRACTION99
3.6195-3.98370.20781520.20372817X-RAY DIFFRACTION100
3.9837-4.56010.17281780.16722786X-RAY DIFFRACTION100
4.5601-5.7450.18041370.16192840X-RAY DIFFRACTION100
5.745-78.32770.19951460.17422889X-RAY DIFFRACTION99

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