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- PDB-4kw5: M. tuberculosis DprE1 in complex with inhibitor TCA1 -

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Basic information

Entry
Database: PDB / ID: 4kw5
TitleM. tuberculosis DprE1 in complex with inhibitor TCA1
ComponentsOxidoreductase
Keywordsoxidoreductase/oxidoreductase INHIBITOR / alpha/beta fold / oxidoreductase / oxidoreductase-oxidoreductase INHIBITOR complex
Function / homologyChem-1W6 / FLAVIN-ADENINE DINUCLEOTIDE / IMIDAZOLE / :
Function and homology information
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.612 Å
AuthorsBatt, S.M. / Besra, G.S. / Futterer, K.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2013
Title: Identification of a small molecule with activity against drug-resistant and persistent tuberculosis.
Authors: Wang, F. / Sambandan, D. / Halder, R. / Wang, J. / Batt, S.M. / Weinrick, B. / Ahmad, I. / Yang, P. / Zhang, Y. / Kim, J. / Hassani, M. / Huszar, S. / Trefzer, C. / Ma, Z. / Kaneko, T. / ...Authors: Wang, F. / Sambandan, D. / Halder, R. / Wang, J. / Batt, S.M. / Weinrick, B. / Ahmad, I. / Yang, P. / Zhang, Y. / Kim, J. / Hassani, M. / Huszar, S. / Trefzer, C. / Ma, Z. / Kaneko, T. / Mdluli, K.E. / Franzblau, S. / Chatterjee, A.K. / Johnson, K. / Mikusova, K. / Besra, G.S. / Futterer, K. / Jacobs, W.R. / Schultz, P.G.
History
DepositionMay 23, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 10, 2013Provider: repository / Type: Initial release
Revision 1.1Jul 17, 2013Group: Database references
Revision 1.2Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Oxidoreductase
B: Oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,10710
Polymers100,4402
Non-polymers2,6678
Water70339
1
A: Oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,5425
Polymers50,2201
Non-polymers1,3224
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,5655
Polymers50,2201
Non-polymers1,3454
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)78.230, 84.190, 81.050
Angle α, β, γ (deg.)90.00, 103.55, 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 1:263)
211chain B AND (resi 1:263)
112chain A and resi 305:313
212chain B and resi 305:313
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

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Protein , 1 types, 2 molecules AB

#1: Protein Oxidoreductase


Mass: 50219.977 Da / Num. of mol.: 2 / Fragment: DprE1 / Mutation: wild-type
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37Rv / Gene: Rv3790, RVBD_3790 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: I6X8C4, decaprenylphospho-beta-D-ribofuranose 2-dehydrogenase

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Non-polymers , 5 types, 47 molecules

#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 2 / Fragment: TCA1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Chemical ChemComp-1W6 / ethyl ({2-[(1,3-benzothiazol-2-ylcarbonyl)amino]thiophen-3-yl}carbonyl)carbamate


Mass: 375.422 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H13N3O4S2
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-IMD / IMIDAZOLE


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


Mass: 18.015 Da / Num. of mol.: 39 / 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: 2.58 Å3/Da / Density % sol: 52.39 %
Crystal growTemperature: 288 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 40 - 43% (w/v) polypropylene glycol 400, 0.1 M imidazole, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 288K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 1, 2012 / Details: mirrors
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.61→84.2 Å / Num. all: 31083 / Num. obs: 31083 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.8 % / Biso Wilson estimate: 62.9 Å2 / Rmerge(I) obs: 0.102 / Rsym value: 0.102 / Net I/σ(I): 13.1
Reflection shellResolution: 2.61→2.68 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.992 / Mean I/σ(I) obs: 2.3 / Rsym value: 0.992 / % possible all: 99

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Processing

Software
NameVersionClassification
GDAdata collection
PHASERphasing
PHENIX(phenix.refine: 1.7.3_928)refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4FEH

4feh


Resolution: 2.612→62.529 Å / SU ML: 0.47 / σ(F): 1.48 / Phase error: 27.65 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2474 1565 5.04 %RANDOM
Rwork0.1894 ---
all0.1924 31059 --
obs0.1924 31059 99.64 %-
Solvent computationShrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 33.454 Å2 / ksol: 0.313 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-4.7465 Å20 Å2-11.2291 Å2
2--5.4087 Å20 Å2
3----10.1552 Å2
Refinement stepCycle: LAST / Resolution: 2.612→62.529 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6347 0 179 39 6565
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0086681
X-RAY DIFFRACTIONf_angle_d1.179105
X-RAY DIFFRACTIONf_dihedral_angle_d16.152357
X-RAY DIFFRACTIONf_chiral_restr0.0761013
X-RAY DIFFRACTIONf_plane_restr0.0061161
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A1847X-RAY DIFFRACTIONPOSITIONAL
12B1847X-RAY DIFFRACTIONPOSITIONAL0.046
21A72X-RAY DIFFRACTIONPOSITIONAL
22B72X-RAY DIFFRACTIONPOSITIONAL0.043
31A1057X-RAY DIFFRACTIONPOSITIONAL
32B1057X-RAY DIFFRACTIONPOSITIONAL0.057
41A53X-RAY DIFFRACTIONPOSITIONAL
42B53X-RAY DIFFRACTIONPOSITIONAL0.032
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6123-2.69670.39071430.31662642X-RAY DIFFRACTION99
2.6967-2.7930.3521340.28932674X-RAY DIFFRACTION100
2.793-2.90490.35471150.2592704X-RAY DIFFRACTION100
2.9049-3.03710.33041440.25192622X-RAY DIFFRACTION100
3.0371-3.19720.32631450.22522676X-RAY DIFFRACTION100
3.1972-3.39750.32361350.22392708X-RAY DIFFRACTION100
3.3975-3.65980.26711510.20942659X-RAY DIFFRACTION100
3.6598-4.0280.23791460.1782669X-RAY DIFFRACTION100
4.028-4.61070.19541470.1342686X-RAY DIFFRACTION100
4.6107-5.80840.17271550.1412707X-RAY DIFFRACTION100
5.8084-62.54660.20651500.16752747X-RAY DIFFRACTION100
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)
11.2295-0.33761.10910.4836-0.16141.41510.0194-0.0949-0.0060.00550.0369-0.03380.0648-0.03470.01170.12910.00010.04750.108-0.03470.181112.5381-10.420636.5466
21.88230.88591.26670.85890.19440.86310.06410.4293-0.0707-0.02380.15860.05740.14920.16560.030.24390.01650.01950.24890.00050.2033-21.4188-17.04960.4758
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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