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- PDB-4p8y: Crystal structure of M. tuberculosis DprE1 in complex with the no... -

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Basic information

Entry
Database: PDB / ID: 4p8y
TitleCrystal structure of M. tuberculosis DprE1 in complex with the non-covalent inhibitor Ty21c
ComponentsProbable decaprenylphosphoryl-beta-D-ribose oxidase
KeywordsOXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR / DprE1 / inhibitor / complex / non-covalent / OXIDOREDUCTASE-OXIDOREDUCTASE INHIBITOR complex
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-38C / FLAVIN-ADENINE DINUCLEOTIDE / IMIDAZOLE / Decaprenylphosphoryl-beta-D-ribose oxidase / Decaprenylphosphoryl-beta-D-ribose oxidase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.01 Å
AuthorsNeres, J. / Pojer, F. / Cole, S.T.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
European Commission260872 Switzerland
CitationJournal: Acs Chem.Biol. / Year: 2015
Title: 2-Carboxyquinoxalines Kill Mycobacterium tuberculosis through Noncovalent Inhibition of DprE1.
Authors: Neres, J. / Hartkoorn, R.C. / Chiarelli, L.R. / Gadupudi, R. / Pasca, M.R. / Mori, G. / Venturelli, A. / Savina, S. / Makarov, V. / Kolly, G.S. / Molteni, E. / Binda, C. / Dhar, N. / ...Authors: Neres, J. / Hartkoorn, R.C. / Chiarelli, L.R. / Gadupudi, R. / Pasca, M.R. / Mori, G. / Venturelli, A. / Savina, S. / Makarov, V. / Kolly, G.S. / Molteni, E. / Binda, C. / Dhar, N. / Ferrari, S. / Brodin, P. / Delorme, V. / Landry, V. / de Jesus Lopes Ribeiro, A.L. / Farina, D. / Saxena, P. / Pojer, F. / Carta, A. / Luciani, R. / Porta, A. / Zanoni, G. / De Rossi, E. / Costi, M.P. / Riccardi, G. / Cole, S.T.
History
DepositionApr 1, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 10, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 4, 2015Group: Derived calculations
Revision 1.2Apr 1, 2015Group: Database references
Revision 1.3Nov 22, 2017Group: Derived calculations / Other ...Derived calculations / Other / Refinement description / Source and taxonomy
Category: entity_src_gen / pdbx_database_status ...entity_src_gen / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_oper_list / software
Item: _entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible ..._entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_oper_list.symmetry_operation / _software.classification
Revision 1.4Dec 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.d_res_low / _refine_hist.number_atoms_solvent / _refine_hist.number_atoms_total / _refine_hist.pdbx_number_atoms_ligand / _refine_hist.pdbx_number_atoms_nucleic_acid / _refine_hist.pdbx_number_atoms_protein

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Probable decaprenylphosphoryl-beta-D-ribose oxidase
B: Probable decaprenylphosphoryl-beta-D-ribose oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,5386
Polymers104,5202
Non-polymers2,0184
Water3,315184
1
A: Probable decaprenylphosphoryl-beta-D-ribose oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,4924
Polymers52,2601
Non-polymers1,2323
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Probable decaprenylphosphoryl-beta-D-ribose oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,0462
Polymers52,2601
Non-polymers7861
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)77.064, 83.312, 80.659
Angle α, β, γ (deg.)90.00, 103.00, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Probable decaprenylphosphoryl-beta-D-ribose oxidase / DprE1


Mass: 52260.133 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37Rv / Gene: dprE1, Rv3790, MT3898 / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P72056, UniProt: P9WJF0*PLUS, Oxidoreductases
#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-38C / 3-[(4-methoxybenzyl)amino]-6-(trifluoromethyl)quinoxaline-2-carboxylic acid


Mass: 377.317 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H14F3N3O3
#4: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H5N2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 184 / 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: 2.41 Å3/Da / Density % sol: 49.04 % / Description: Rmeas 0.043 (overall), 0.321 (outer shell)
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.2 / Details: 42% Polyproylene glycol 400, 100 mM imidazole

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Jun 24, 2013
RadiationMonochromator: Bartels monochromator with dual channel cut crystals
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.01→42.3 Å / Num. obs: 122280 / % possible obs: 93.7 % / Redundancy: 2.2 % / Net I/σ(I): 15.8
Reflection shellResolution: 2.01→2.13 Å / Redundancy: 2.2 % / Mean I/σ(I) obs: 3.57 / % possible all: 89.7

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Processing

Software
NameVersionClassification
XDSdata scaling
PHASERphasing
REFMAC5.6.0117refinement
RefinementResolution: 2.01→42.3 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.933 / SU B: 4.879 / SU ML: 0.134 / Cross valid method: THROUGHOUT / ESU R: 0.201 / ESU R Free: 0.175 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.24823 3202 5 %RANDOM
Rwork0.20862 ---
obs0.21061 60817 96.43 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 40.493 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20.02 Å2
2---0.01 Å20 Å2
3---0.02 Å2
Refinement stepCycle: 1 / Resolution: 2.01→42.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6693 0 138 184 7015
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0197035
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2231.9789585
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7775876
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.17422.676299
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.121151093
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.1761560
X-RAY DIFFRACTIONr_chiral_restr0.0880.21056
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0215372
X-RAY DIFFRACTIONr_gen_planes_other
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.01→2.061 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.322 220 -
Rwork0.308 4164 -
obs--91.33 %

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