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- PDB-5mtr: Crystal structure of M. tuberculosis InhA inhibited by PT512 -

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Basic information

Entry
Database: PDB / ID: 5mtr
TitleCrystal structure of M. tuberculosis InhA inhibited by PT512
ComponentsEnoyl-[acyl-carrier-protein] reductase [NADH]
KeywordsOXIDOREDUCTASE / bacterial enoyl-ACP reductase / diphenylether / residence time
Function / homology
Function and homology information


trans-2-enoyl-CoA reductase (NADH) activity / mycolic acid biosynthetic process / fatty acid elongation / enoyl-[acyl-carrier-protein] reductase (NADH) / enoyl-[acyl-carrier-protein] reductase (NADH) activity / NAD+ binding / peptidoglycan-based cell wall / fatty acid binding / response to antibiotic / plasma membrane
Similarity search - Function
: / Enoyl-[acyl-carrier-protein] reductase (NADH) / Enoyl-(Acyl carrier protein) reductase / Short-chain dehydrogenase/reductase SDR / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Chem-XT0 / Enoyl-[acyl-carrier-protein] reductase [NADH]
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsEltschkner, S. / Pschibul, A. / Spagnuolo, L.A. / Yu, W. / Tonge, P.J. / Kisker, C.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research FoundationSFB 630 Germany
CitationJournal: J. Am. Chem. Soc. / Year: 2017
Title: Evaluating the Contribution of Transition-State Destabilization to Changes in the Residence Time of Triazole-Based InhA Inhibitors.
Authors: Spagnuolo, L.A. / Eltschkner, S. / Yu, W. / Daryaee, F. / Davoodi, S. / Knudson, S.E. / Allen, E.K. / Merino, J. / Pschibul, A. / Moree, B. / Thivalapill, N. / Truglio, J.J. / Salafsky, J. / ...Authors: Spagnuolo, L.A. / Eltschkner, S. / Yu, W. / Daryaee, F. / Davoodi, S. / Knudson, S.E. / Allen, E.K. / Merino, J. / Pschibul, A. / Moree, B. / Thivalapill, N. / Truglio, J.J. / Salafsky, J. / Slayden, R.A. / Kisker, C. / Tonge, P.J.
History
DepositionJan 10, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 15, 2017Provider: repository / Type: Initial release
Revision 1.1Mar 22, 2017Group: Database references
Revision 1.2Sep 6, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Jan 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Enoyl-[acyl-carrier-protein] reductase [NADH]
B: Enoyl-[acyl-carrier-protein] reductase [NADH]
E: Enoyl-[acyl-carrier-protein] reductase [NADH]
G: Enoyl-[acyl-carrier-protein] reductase [NADH]
C: Enoyl-[acyl-carrier-protein] reductase [NADH]
D: Enoyl-[acyl-carrier-protein] reductase [NADH]
F: Enoyl-[acyl-carrier-protein] reductase [NADH]
H: Enoyl-[acyl-carrier-protein] reductase [NADH]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)254,07126
Polymers245,8098
Non-polymers8,26218
Water22,4471246
1
A: Enoyl-[acyl-carrier-protein] reductase [NADH]
B: Enoyl-[acyl-carrier-protein] reductase [NADH]
E: Enoyl-[acyl-carrier-protein] reductase [NADH]
G: Enoyl-[acyl-carrier-protein] reductase [NADH]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)127,00012
Polymers122,9054
Non-polymers4,0958
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19220 Å2
ΔGint-123 kcal/mol
Surface area33180 Å2
MethodPISA
2
C: Enoyl-[acyl-carrier-protein] reductase [NADH]
D: Enoyl-[acyl-carrier-protein] reductase [NADH]
F: Enoyl-[acyl-carrier-protein] reductase [NADH]
H: Enoyl-[acyl-carrier-protein] reductase [NADH]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)127,07114
Polymers122,9054
Non-polymers4,16610
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19410 Å2
ΔGint-142 kcal/mol
Surface area33020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.590, 92.229, 180.531
Angle α, β, γ (deg.)90.00, 96.05, 90.00
Int Tables number3
Space group name H-MP121

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Components

#1: Protein
Enoyl-[acyl-carrier-protein] reductase [NADH] / Enoyl-ACP reductase / FAS-II enoyl-ACP reductase / NADH-dependent 2-trans-enoyl-ACP reductase


Mass: 30726.131 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Details: SBL not fully ordered, aa 205 - 207 missing / Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: inhA, Rv1484, MTCY277.05 / Production host: Escherichia coli (E. coli)
References: UniProt: P9WGR1, enoyl-[acyl-carrier-protein] reductase (NADH)
#2: Chemical
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Chemical
ChemComp-XT0 / 2-[4-[(4-cyclopentyl-1,2,3-triazol-1-yl)methyl]-2-oxidanyl-phenoxy]benzenecarbonitrile / PT512


Mass: 360.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C21H20N4O2
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1246 / 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: 3.21 Å3/Da / Density % sol: 61.7 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 1.6 M sodium acetate, pH 7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.918409 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 14, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918409 Å / Relative weight: 1
ReflectionResolution: 2→58.33 Å / Num. obs: 155047 / % possible obs: 80.3 % / Redundancy: 2.9 % / CC1/2: 0.988 / Rmerge(I) obs: 0.103 / Rpim(I) all: 0.072 / Net I/σ(I): 6.4
Reflection shellResolution: 2→2.03 Å / Redundancy: 2.9 % / Mean I/σ(I) obs: 1.9 / Num. unique obs: 6972 / CC1/2: 0.446 / % possible all: 73.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0155refinement
MOSFLM5.8.0155data reduction
Aimlessdata scaling
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2x23

2x23


Resolution: 2→58.33 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.923 / SU B: 0.002 / SU ML: 0 / Cross valid method: THROUGHOUT / ESU R: 0.156 / ESU R Free: 0.178 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23406 7736 5 %RANDOM
Rwork0.20503 ---
obs0.20648 147299 80.33 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 26.554 Å2
Baniso -1Baniso -2Baniso -3
1-0.59 Å20 Å20.79 Å2
2---0.9 Å20 Å2
3---0.13 Å2
Refinement stepCycle: 1 / Resolution: 2→58.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15857 0 570 1246 17673
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.328 514 -
Rwork0.324 9890 -
obs--73.27 %

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