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- PDB-7umw: Crystal structure of E. Coli FabI in complex with NAD and Fabimyc... -

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Basic information

Entry
Database: PDB / ID: 7umw
TitleCrystal structure of E. Coli FabI in complex with NAD and Fabimycin ((S,E)-3-(7-amino-8-oxo-6,7,8,9-tetrahydro-5H-pyrido[2,3-b]azepin-3-yl)-N-methyl-N-((3-methylbenzofuran-2-yl)methyl)acrylamide)
ComponentsEnoyl-[acyl-carrier-protein] reductase [NADH] FabI
KeywordsANTIBIOTIC / enoyl reductase / FabI / antimicrobial resistance
Function / homology
Function and homology information


enoyl-[acyl-carrier-protein] reductase activity (NAD(P)H) / NADH binding / biotin biosynthetic process / fatty acid elongation / enoyl-[acyl-carrier-protein] reductase (NADH) / enoyl-[acyl-carrier-protein] reductase (NADH) activity / lipid biosynthetic process / catalytic complex / protein homotetramerization / response to antibiotic ...enoyl-[acyl-carrier-protein] reductase activity (NAD(P)H) / NADH binding / biotin biosynthetic process / fatty acid elongation / enoyl-[acyl-carrier-protein] reductase (NADH) / enoyl-[acyl-carrier-protein] reductase (NADH) activity / lipid biosynthetic process / catalytic complex / protein homotetramerization / response to antibiotic / protein-containing complex / identical protein binding / membrane / cytosol
Similarity search - Function
Enoyl-[acyl-carrier-protein] reductase (NADH) / Enoyl-(Acyl carrier protein) reductase / Short-chain dehydrogenase/reductase SDR / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Chem-NUC / Enoyl-[acyl-carrier-protein] reductase [NADH] FabI
Similarity search - Component
Biological speciesEscherichia coli str. K-12 substr. MG1655 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.54 Å
AuthorsHajian, B.
Funding support United States, 1items
OrganizationGrant numberCountry
Other private United States
Citation
Journal: Acs Cent.Sci. / Year: 2022
Title: An Iterative Approach Guides Discovery of the FabI Inhibitor Fabimycin, a Late-Stage Antibiotic Candidate with In Vivo Efficacy against Drug-Resistant Gram-Negative Infections
Authors: Parker, E.N. / Cain, B.N. / Hajian, B. / Ulrich, R.J. / Geddes, E.J. / Barkho, S. / Lee, H.Y. / Williams, J.D. / Raynor, M. / Caridha, D. / Zaino, A. / Rohde, J.M. / Zak, M. / Shekhar, M. / ...Authors: Parker, E.N. / Cain, B.N. / Hajian, B. / Ulrich, R.J. / Geddes, E.J. / Barkho, S. / Lee, H.Y. / Williams, J.D. / Raynor, M. / Caridha, D. / Zaino, A. / Rohde, J.M. / Zak, M. / Shekhar, M. / Munoz, K.A. / Rzasa, K.M. / Temple, E.R. / Hunt, D. / Jin, X. / Vuong, C. / Pannone, K. / Kelly, A.M. / Mulligan, M.P. / Lee, K.K. / Lau, G.W. / Hung, D.T. / Hergenrother, P.J.
#1: Journal: Acs Cent.Sci. / Year: 2022
Title: An Iterative Approach Guides Discovery of the FabI Inhibitor Fabimycin, a Late-Stage Antibiotic Candidate with In Vivo Efficacy against Drug-Resistant Gram-Negative Infections.
Authors: Parker, E.N. / Cain, B.N. / Hajian, B. / Ulrich, R.J. / Geddes, E.J. / Barkho, S. / Lee, H.Y. / Williams, J.D. / Raynor, M. / Caridha, D. / Zaino, A. / Shekhar, M. / Munoz, K.A. / Rzasa, K.M. ...Authors: Parker, E.N. / Cain, B.N. / Hajian, B. / Ulrich, R.J. / Geddes, E.J. / Barkho, S. / Lee, H.Y. / Williams, J.D. / Raynor, M. / Caridha, D. / Zaino, A. / Shekhar, M. / Munoz, K.A. / Rzasa, K.M. / Temple, E.R. / Hunt, D. / Jin, X. / Vuong, C. / Pannone, K. / Kelly, A.M. / Mulligan, M.P. / Lee, K.K. / Lau, G.W. / Hung, D.T. / Hergenrother, P.J.
History
DepositionApr 8, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 14, 2022Provider: repository / Type: Initial release
Revision 1.1Feb 15, 2023Group: Database references / Category: citation / citation_author
Revision 1.2Aug 16, 2023Group: Data collection / Source and taxonomy / Category: chem_comp_atom / chem_comp_bond / entity_src_gen
Item: _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name
Revision 1.3Oct 25, 2023Group: Refinement description / Category: pdbx_initial_refinement_model

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


Theoretical massNumber of molelcules
Total (without water)58,6566
Polymers56,5212
Non-polymers2,1364
Water6,359353
1
A: Enoyl-[acyl-carrier-protein] reductase [NADH] FabI
B: Enoyl-[acyl-carrier-protein] reductase [NADH] FabI
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)117,31312
Polymers113,0414
Non-polymers4,2728
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_554-y,-x,-z-1/61
Buried area20100 Å2
ΔGint-121 kcal/mol
Surface area30330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.540, 79.540, 323.680
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122
Space group name HallP612(x,y,z+5/12)
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/6
#3: y,-x+y,z+5/6
#4: -y,x-y,z+1/3
#5: -x+y,-x,z+2/3
#6: x-y,-y,-z
#7: -x,-x+y,-z+2/3
#8: -x,-y,z+1/2
#9: y,x,-z+1/3
#10: -y,-x,-z+5/6
#11: -x+y,y,-z+1/2
#12: x,x-y,-z+1/6
Components on special symmetry positions
IDModelComponents
11A-526-

HOH

21B-505-

HOH

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Components

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


Mass: 28260.266 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli str. K-12 substr. MG1655 (bacteria)
Gene: fabI / Production host: Escherichia coli (E. coli)
References: UniProt: P0AEK4, enoyl-[acyl-carrier-protein] reductase (NADH)
#2: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Chemical ChemComp-NUC / (2E)-3-[(7S)-7-amino-8-oxo-6,7,8,9-tetrahydro-5H-pyrido[2,3-b]azepin-3-yl]-N-methyl-N-[(3-methyl-1-benzofuran-2-yl)methyl]prop-2-enamide


Mass: 404.462 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C23H24N4O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 353 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.61 Å3/Da / Density % sol: 52.96 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 100 mM Tris pH 7.5-8.5 0.5-1.5 M sodium citrate tribasic.

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Data collection

DiffractionMean temperature: 193 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-2 / Wavelength: 0.9793 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 23, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.54→58.06 Å / Num. obs: 156032 / % possible obs: 93.92 % / Redundancy: 2 % / Biso Wilson estimate: 11.25 Å2 / CC1/2: 0.999 / Net I/σ(I): 16.06
Reflection shellResolution: 1.54→1.595 Å / Num. unique obs: 6889 / CC1/2: 0.913

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Processing

Software
NameVersionClassification
Aimlessdata scaling
PHENIX1.19.2_4158refinement
XDSdata reduction
Cootmodel building
PDB_EXTRACTdata extraction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4JQC

4jqc


Resolution: 1.54→58.06 Å / SU ML: 0.2109 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.4761
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2447 3656 2.34 %
Rwork0.2135 152376 -
obs0.2143 156032 91.65 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 21.23 Å2
Refinement stepCycle: LAST / Resolution: 1.54→58.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3829 0 148 353 4330
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00944071
X-RAY DIFFRACTIONf_angle_d1.26515532
X-RAY DIFFRACTIONf_chiral_restr0.0656623
X-RAY DIFFRACTIONf_plane_restr0.0096710
X-RAY DIFFRACTIONf_dihedral_angle_d6.4625579
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.54-1.560.29481040.2844545X-RAY DIFFRACTION70.09
1.56-1.580.28731140.27164742X-RAY DIFFRACTION75
1.58-1.60.30421180.28094970X-RAY DIFFRACTION77.02
1.6-1.630.27461190.27954942X-RAY DIFFRACTION77.52
1.63-1.650.31651220.27635227X-RAY DIFFRACTION81.88
1.65-1.680.30961350.27675360X-RAY DIFFRACTION84.1
1.68-1.710.34321320.2765403X-RAY DIFFRACTION84.7
1.71-1.740.27871280.27865505X-RAY DIFFRACTION85.61
1.74-1.770.32751370.26935570X-RAY DIFFRACTION87.21
1.77-1.810.3651330.27535687X-RAY DIFFRACTION88.8
1.81-1.850.31891400.2685776X-RAY DIFFRACTION90.42
1.85-1.890.28721400.25775913X-RAY DIFFRACTION92.48
1.89-1.940.27951440.24636066X-RAY DIFFRACTION94.58
1.94-1.990.29431530.23826193X-RAY DIFFRACTION96.96
1.99-2.050.23831540.23826237X-RAY DIFFRACTION98.19
2.05-2.110.2981530.22586312X-RAY DIFFRACTION99.32
2.11-2.190.23811490.2226402X-RAY DIFFRACTION99.5
2.19-2.280.25691520.21936393X-RAY DIFFRACTION99.85
2.28-2.380.2591530.21746364X-RAY DIFFRACTION99.97
2.38-2.510.21471530.226423X-RAY DIFFRACTION100
2.51-2.660.23031560.21196387X-RAY DIFFRACTION99.98
2.66-2.870.22231580.20386376X-RAY DIFFRACTION100
2.87-3.160.24061530.20456386X-RAY DIFFRACTION100
3.16-3.620.21961500.17876426X-RAY DIFFRACTION100
3.62-4.560.20371480.14246368X-RAY DIFFRACTION100
4.56-58.060.14611580.15036403X-RAY DIFFRACTION99.98
Refinement TLS params.Method: refined / Origin x: -35.8600580592 Å / Origin y: 35.5684760772 Å / Origin z: -18.7602826598 Å
111213212223313233
T0.0274931588424 Å20.028973844603 Å2-0.00394228064055 Å2-0.0543352959542 Å2-0.0301457757974 Å2--0.0698610269887 Å2
L0.631802882406 °20.704416799374 °20.709265846054 °2-1.21000918338 °21.07534204287 °2--1.22396520934 °2
S-0.0399209291554 Å °0.0292922777422 Å °-0.00922176574213 Å °0.00944137160867 Å °0.0488095727979 Å °-0.0083330046105 Å °-0.111053384194 Å °0.171662661408 Å °0.0487172318942 Å °
Refinement TLS groupSelection details: all

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