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- PDB-4oyr: Competition of the small inhibitor PT91 with large fatty acyl sub... -

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Basic information

Entry
Database: PDB / ID: 4oyr
TitleCompetition of the small inhibitor PT91 with large fatty acyl substrate of the Mycobacterium tuberculosis enoyl-ACP reductase InhA by induced substrate-binding loop refolding
ComponentsEnoyl-[acyl-carrier-protein] reductase [NADH]
KeywordsOXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR / Bacterial fatty acid biosynthesis / enzyme-inhibitor complex / substrate-binding loop refolding / induced-fit / 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
2-(2-chloranylphenoxy)-5-hexyl-phenol / 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: 2.2995 Å
AuthorsLi, H.J. / Pan, P. / Lai, C.T. / Liu, N. / Garcia-Diaz, M. / Simmerling, C. / Tonge, P.J.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM102864 United States
Department of Energy (DOE, United States) United States
National Institutes of Health/National Center for Research Resources (NIH/NCRR)P41RR012408 United States
CitationJournal: Acs Chem.Biol. / Year: 2014
Title: A Structural and Energetic Model for the Slow-Onset Inhibition of the Mycobacterium tuberculosis Enoyl-ACP Reductase InhA.
Authors: Li, H.J. / Lai, C.T. / Pan, P. / Yu, W. / Liu, N. / Bommineni, G.R. / Garcia-Diaz, M. / Simmerling, C. / Tonge, P.J.
History
DepositionFeb 13, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 30, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 6, 2017Group: Advisory / Author supporting evidence ...Advisory / Author supporting evidence / Derived calculations / Other / Refinement description / Source and taxonomy / Structure summary
Category: entity_src_gen / pdbx_audit_support ...entity_src_gen / pdbx_audit_support / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list / pdbx_unobs_or_zero_occ_atoms / software / struct_keywords / struct_site
Item: _entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization ..._entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_assembly_prop.type / _pdbx_struct_assembly_prop.value / _pdbx_struct_oper_list.symmetry_operation / _struct_keywords.text / _struct_site.details
Revision 1.2Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Sep 27, 2023Group: 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 / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.number_atoms_total / _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: Enoyl-[acyl-carrier-protein] reductase [NADH]
B: Enoyl-[acyl-carrier-protein] reductase [NADH]
C: Enoyl-[acyl-carrier-protein] reductase [NADH]
D: Enoyl-[acyl-carrier-protein] reductase [NADH]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)126,77712
Polymers122,9054
Non-polymers3,8738
Water2,000111
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18350 Å2
ΔGint-127 kcal/mol
Surface area31390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.842, 90.653, 164.436
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 30726.131 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: MT1531,MTCY277.05,Rv1484,inhA / 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 / Nicotinamide adenine dinucleotide


Mass: 663.425 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Chemical
ChemComp-1US / 2-(2-chloranylphenoxy)-5-hexyl-phenol


Mass: 304.811 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C18H21ClO2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 111 / 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: 2.45 Å3/Da / Density % sol: 49.86 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.8
Details: 100 mM ADA, 200 mM ammonium acetate, 16% PEG 4000, 6% DMSO

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Mar 6, 2009
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.2995→50 Å / Num. obs: 45551 / % possible obs: 90.1 % / Redundancy: 4.2 % / Biso Wilson estimate: 36.78 Å2 / Rmerge(I) obs: 0.062 / Χ2: 1.147 / Net I/av σ(I): 20.87 / Net I/σ(I): 12 / Num. measured all: 189983
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.2995-2.343.50.35221651.12486.5
2.34-2.383.90.30322401.12390.8
2.38-2.434.20.31422671.15491.1
2.43-2.484.40.28822711.15591.4
2.48-2.534.40.28423051.19191.9
2.53-2.594.30.23322751.17190.7
2.59-2.664.40.19522761.25591.1
2.66-2.734.30.17322341.23589.9
2.73-2.814.20.15822401.27190.2
2.81-2.94.20.12522481.2989.6
2.9-34.20.10722221.17388.2
3-3.124.20.09922241.18188.2
3.12-3.264.20.07722201.12888.3
3.26-3.4440.06622331.0988.6
3.44-3.6540.05622011.16587.3
3.65-3.9340.04922071.11286.4
3.93-4.333.90.04321911.04286.6
4.33-4.9540.0422720.96588.2
4.95-6.244.20.03725601.17297.9
6.24-504.70.02827000.95498.6

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation3 Å43.7 Å
Translation3 Å43.7 Å

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Processing

Software
NameVersionClassification
HKL-2000data collection
HKL-2000data scaling
PHENIXrefinement
PDB_EXTRACT3.14data extraction
CNSrefinement
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2X23

2x23


Resolution: 2.2995→43.697 Å / FOM work R set: 0.7725 / SU ML: 0.71 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 28.47 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.244 2282 5.03 %
Rwork0.1941 43119 -
obs0.1967 45401 89.83 %
Solvent computationShrinkage radii: 1.11 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 41.378 Å2 / ksol: 0.345 e/Å3
Displacement parametersBiso max: 103 Å2 / Biso mean: 45.43 Å2 / Biso min: 16 Å2
Baniso -1Baniso -2Baniso -3
1-18.4432 Å2-0 Å2-0 Å2
2---10.9631 Å2-0 Å2
3----7.48 Å2
Refinement stepCycle: final / Resolution: 2.2995→43.697 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7490 0 254 111 7855
Biso mean--44.9 37.63 -
Num. residues----1056
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0078014
X-RAY DIFFRACTIONf_angle_d1.12310918
X-RAY DIFFRACTIONf_chiral_restr0.071207
X-RAY DIFFRACTIONf_plane_restr0.0051376
X-RAY DIFFRACTIONf_dihedral_angle_d16.9432952
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 16

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.2995-2.34940.32191410.24112528266985
2.3494-2.40410.29191390.2072674281391
2.4041-2.46420.29651370.20732692282992
2.4642-2.53080.32451280.20762737286592
2.5308-2.60530.28831380.20442688282691
2.6053-2.68940.27481590.20362671283091
2.6894-2.78550.27921440.22522661280590
2.7855-2.8970.28661350.21452656279190
2.897-3.02880.27481540.21122615276988
3.0288-3.18840.29311350.21342641277688
3.1884-3.38810.27591230.19112637276088
3.3881-3.64960.2651390.20352634277388
3.6496-4.01670.22141450.18222616276187
4.0167-4.59730.18971350.16172610274586
4.5973-5.790.21061570.17972890304794
5.79-43.70470.20851730.19283169334299
Refinement TLS params.Method: refined / Origin x: -9.7427 Å / Origin y: 2.5004 Å / Origin z: 21.1845 Å
111213212223313233
T0.2252 Å20.0766 Å2-0.1129 Å2-0.1301 Å2-0.0287 Å2--0.1376 Å2
L0.299 °20.0637 °20.0744 °2-1.3426 °20.3837 °2--0.7352 °2
S-0.0168 Å °0.0379 Å °0.0804 Å °-0.2577 Å °-0.1037 Å °0.1995 Å °-0.2512 Å °-0.1814 Å °0.0889 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA3 - 269
2X-RAY DIFFRACTION1allB3 - 269
3X-RAY DIFFRACTION1allC2 - 269
4X-RAY DIFFRACTION1allD2 - 269
5X-RAY DIFFRACTION1allA301 - 302
6X-RAY DIFFRACTION1allB301 - 302
7X-RAY DIFFRACTION1allC301 - 302
8X-RAY DIFFRACTION1allD301 - 302
9X-RAY DIFFRACTION1allA401 - 444
10X-RAY DIFFRACTION1allB401 - 431
11X-RAY DIFFRACTION1allC401 - 428
12X-RAY DIFFRACTION1allD401 - 408

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