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- PDB-6hfw: Mycobacterium tuberculosis DprE1 in complex with CMP1 -

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Basic information

Entry
Database: PDB / ID: 6hfw
TitleMycobacterium tuberculosis DprE1 in complex with CMP1
ComponentsDecaprenylphosphoryl-beta-D-ribose oxidase
KeywordsOXIDOREDUCTASE / OXIDOREDUCTASE INHIBITOR
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-G1T / IMIDAZOLE / Decaprenylphosphoryl-beta-D-ribose oxidase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.47 Å
AuthorsChung, C.
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 1.0Sep 19, 2018Provider: repository / Type: Initial release

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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)106,0087
Polymers103,6772
Non-polymers2,3315
Water4,107228
1
A: Decaprenylphosphoryl-beta-D-ribose oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,0394
Polymers51,8391
Non-polymers1,2003
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Decaprenylphosphoryl-beta-D-ribose oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,9703
Polymers51,8391
Non-polymers1,1312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)78.340, 84.730, 80.900
Angle α, β, γ (deg.)90.00, 103.20, 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: 51838.664 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria)
Strain: ATCC 25618 / H37Rv / Gene: dprE1, Rv3790 / Production host: Escherichia coli (E. coli)
References: UniProt: P9WJF1, 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-IMD / IMIDAZOLE / Imidazole


Mass: 69.085 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H5N2
#4: Chemical ChemComp-G1T / 8-(oxidanylamino)-2-piperidin-1-yl-6-(trifluoromethyl)-1,3-benzothiazin-4-one


Mass: 345.340 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H14F3N3O2S
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 228 / 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: 2.52 Å3/Da / Density % sol: 51.22 %
Crystal growTemperature: 298 K / Method: microbatch / Details: 20mM in 30% PPG, 100mM Imidazole,pH 7.4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.0725 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 25, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0725 Å / Relative weight: 1
ReflectionResolution: 2.47→56.69 Å / Num. obs: 33896 / % possible obs: 96.8 % / Redundancy: 2.9 % / Net I/σ(I): 11.3
Reflection shellResolution: 2.47→2.6 Å

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Processing

Software
NameVersionClassification
REFMAC5.6.0117refinement
SCALAdata scaling
RefinementResolution: 2.47→56.69 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.942 / SU B: 15.939 / SU ML: 0.173 / Cross valid method: THROUGHOUT / ESU R: 0.441 / ESU R Free: 0.252 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22027 1776 5 %RANDOM
Rwork0.16782 ---
obs0.17042 33896 96.08 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 55.09 Å2
Baniso -1Baniso -2Baniso -3
1--0.56 Å20 Å2-2.27 Å2
2--0.86 Å20 Å2
3----1.34 Å2
Refinement stepCycle: 1 / Resolution: 2.47→56.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6478 0 157 228 6863
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.026794
X-RAY DIFFRACTIONr_bond_other_d0.0010.024552
X-RAY DIFFRACTIONr_angle_refined_deg1.1921.989253
X-RAY DIFFRACTIONr_angle_other_deg0.855311005
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5725837
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.21222.587286
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.308151038
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.8951558
X-RAY DIFFRACTIONr_chiral_restr0.0630.21028
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0217548
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021462
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: 2.47→2.534 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.437 110 -
Rwork0.37 2465 -
obs--96.12 %
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)
10.6591-0.13380.56340.34340.09540.64540.0565-0.05-0.0083-0.01230.0136-0.03410.0337-0.0333-0.07010.1763-0.0027-0.0680.177-0.02880.114812.8592-12.54736.6175
21.26370.35160.86080.17970.06071.05890.17660.26220.01020.07290.0810.08640.18690.1665-0.25760.2070.0054-0.08690.21270.01850.1586-21.652-18.98720.6835
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A7 - 502
2X-RAY DIFFRACTION2B7 - 502

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