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- PDB-4oim: Crystal structure of Mycobacterium tuberculosis InhA in complex w... -

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Basic information

Entry
Database: PDB / ID: 4oim
TitleCrystal structure of Mycobacterium tuberculosis InhA in complex with inhibitor PT119 in 2.4 M acetate
ComponentsEnoyl-[acyl-carrier-protein] reductase [NADH]
KeywordsOXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR / Inhibition / High-concentration acetate / slow-onset inhibition / substrate binding loop conformational heterogeneity / OXIDOREDUCTASE-OXIDOREDUCTASE INHIBITOR complex
Function / homology
Function and homology information


enoyl-[acyl-carrier-protein] reductase activity (NAD(P)H) / 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 / fatty acid biosynthetic process ...enoyl-[acyl-carrier-protein] reductase activity (NAD(P)H) / 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 / fatty acid biosynthetic process / response to antibiotic / plasma membrane
Similarity search - Function
Enoyl-[acyl-carrier-protein] reductase (NADH) / Enoyl-(Acyl carrier protein) reductase / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / 2-(2-CYANOPHENOXY)-5-HEXYLPHENOL / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Enoyl-[acyl-carrier-protein] reductase [NADH] / Enoyl-[acyl-carrier-protein] reductase [NADH]
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.848 Å
AuthorsLi, H.J. / Pan, P. / Lai, C.T. / Liu, N. / Garcia-Diaz, M. / Simmerling, C. / Tonge, P.J.
Citation
Journal: Chemmedchem / Year: 2014
Title: Time-Dependent Diaryl Ether Inhibitors of InhA: Structure-Activity Relationship Studies of Enzyme Inhibition, Antibacterial Activity, and in vivo Efficacy.
Authors: Pan, P. / Knudson, S.E. / Bommineni, G.R. / Li, H.J. / Lai, C.T. / Liu, N. / Garcia-Diaz, M. / Simmerling, C. / Patil, S.S. / Slayden, R.A. / Tonge, P.J.
#1: Journal: To be Published
Title: A Structural and energetic model for the slow-onset inhibition of InhA, an enzyme drug target from Mycobacterium tuberculosis
Authors: Li, H.J. / Lai, C.T. / Pan, P. / Yu, W. / Liu, N. / Garcia-Diaz, M. / Simmerling, C. / Tonge, P.J.
History
DepositionJan 20, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 23, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
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 / pdbx_struct_special_symmetry / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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: Enoyl-[acyl-carrier-protein] reductase [NADH]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,33414
Polymers30,7261
Non-polymers1,60813
Water1,35175
1
A: Enoyl-[acyl-carrier-protein] reductase [NADH]
hetero molecules

A: Enoyl-[acyl-carrier-protein] reductase [NADH]
hetero molecules

A: Enoyl-[acyl-carrier-protein] reductase [NADH]
hetero molecules

A: Enoyl-[acyl-carrier-protein] reductase [NADH]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)129,33856
Polymers122,9054
Non-polymers6,43352
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-y,-x,-z1
crystal symmetry operation10_555-x,-y,z1
crystal symmetry operation15_555y,x,-z1
Buried area27110 Å2
ΔGint-158 kcal/mol
Surface area31930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.622, 90.622, 182.634
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number98
Space group name H-MI4122
Components on special symmetry positions
IDModelComponents
11A-418-

HOH

21A-451-

HOH

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Components

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


Mass: 30726.131 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: inhA, Rv1484, MT1531, MTCY277.05 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS
References: UniProt: P0A5Y6, UniProt: P9WGR1*PLUS, enoyl-[acyl-carrier-protein] reductase (NADH)
#2: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Chemical ChemComp-JUS / 2-(2-CYANOPHENOXY)-5-HEXYLPHENOL


Mass: 295.376 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H21NO2
#4: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C2H3O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 75 / 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: 3.05 Å3/Da / Density % sol: 59.68 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 2.4 M sodium acetate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 20, 2009
RadiationMonochromator: Double silicon(111) crystal sagittal focusing
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 1.85→50 Å / Num. obs: 32854 / % possible obs: 99.8 % / Redundancy: 14.1 % / Biso Wilson estimate: 29.61 Å2 / Rmerge(I) obs: 0.062 / Χ2: 0.941 / Net I/σ(I): 13.9
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.85-1.8813.30.6816060.7461100
1.88-1.9214.10.57916160.771100
1.92-1.9514.30.4916220.7291100
1.95-1.9914.40.38716240.7531100
1.99-2.0414.40.30516000.7671100
2.04-2.0814.40.25816230.7911100
2.08-2.1414.40.22116260.8161100
2.14-2.1914.50.16316190.8681100
2.19-2.2614.40.13416390.9441100
2.26-2.3314.40.11816360.9111100
2.33-2.4114.40.09716180.9831100
2.41-2.5114.40.08916331.0051100
2.51-2.6314.30.07716461.061100
2.63-2.7614.30.06516341.0181100
2.76-2.9414.20.0616561.0621100
2.94-3.1614.20.06116471.1521100
3.16-3.4814.10.06216741.1681100
3.48-3.9913.70.05316721.1791100
3.99-5.0213.20.03716940.97199.9
5.02-5013.10.03317691.104197.4

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
PHENIX1.7.2_869refinement
PDB_EXTRACT3.14data extraction
CBASSdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2X23

2x23


Resolution: 1.848→45.311 Å / FOM work R set: 0.891 / SU ML: 0.39 / σ(F): 1.34 / Phase error: 17.22 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1981 1633 4.98 %Random
Rwork0.1702 ---
obs0.1716 32823 99.48 %-
Solvent computationShrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 43.612 Å2 / ksol: 0.362 e/Å3
Displacement parametersBiso max: 96.04 Å2 / Biso mean: 39.94 Å2 / Biso min: 17.23 Å2
Baniso -1Baniso -2Baniso -3
1-3.5162 Å20 Å2-0 Å2
2--3.5162 Å2-0 Å2
3----7.0324 Å2
Refinement stepCycle: LAST / Resolution: 1.848→45.311 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1923 0 110 75 2108
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072214
X-RAY DIFFRACTIONf_angle_d1.1433017
X-RAY DIFFRACTIONf_chiral_restr0.071338
X-RAY DIFFRACTIONf_plane_restr0.006381
X-RAY DIFFRACTIONf_dihedral_angle_d14.24801
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.8477-1.9020.25561320.21322441257396
1.902-1.96340.20981440.187625612705100
1.9634-2.03360.19641210.174925892710100
2.0336-2.1150.19291400.165125692709100
2.115-2.21130.18661470.150325812728100
2.2113-2.32790.17751480.158925822730100
2.3279-2.47370.19231260.164525872713100
2.4737-2.66470.22191480.179125952743100
2.6647-2.93280.19781420.183726082750100
2.9328-3.35710.22421110.173926512762100
3.3571-4.2290.20011250.161526712796100
4.229-45.32460.18271490.172755290498
Refinement TLS params.Method: refined / Origin x: 0.6033 Å / Origin y: -21.2614 Å / Origin z: 5.689 Å
111213212223313233
T0.5016 Å20.0017 Å2-0.0646 Å2-0.1302 Å20.0376 Å2--0.2608 Å2
L1.6589 °2-0.1914 °20.0328 °2-1.3739 °2-0.1332 °2--2.6844 °2
S0.0981 Å °-0.1699 Å °-0.3382 Å °0.1569 Å °0.0554 Å °0.0109 Å °0.9478 Å °0.0319 Å °-0.1237 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA2 - 313
2X-RAY DIFFRACTION1allA1 - 475

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