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- PDB-7um8: Crystal structure of E. Coli FabI in complex with NAD and (R,E)-3... -

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Basic information

Entry
Database: PDB / ID: 7um8
TitleCrystal structure of E. Coli FabI in complex with NAD and (R,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-NQF / 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: 1.7 Å
AuthorsHajian, B.
Funding support United States, 1items
OrganizationGrant numberCountry
Other private United States
CitationJournal: 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.
History
DepositionApr 6, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 15, 2023Provider: repository / Type: Initial release
Revision 1.1Aug 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 1.2Oct 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
Water9,332518
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
Unit cell
Length a, b, c (Å)79.630, 79.630, 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-539-

HOH

21B-527-

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 / Feature type: SUBJECT OF INVESTIGATION / Comment: NAD*YM
#3: Chemical ChemComp-NQF / (2E)-3-[(7R)-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.: 518 / 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: 2.62 Å3/Da / Density % sol: 53.07 %
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: 1.7→47.2 Å / Num. obs: 69000 / % possible obs: 99.98 % / Redundancy: 2 % / Biso Wilson estimate: 22.85 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.018 / Net I/σ(I): 19.55
Reflection shellResolution: 1.7→1.761 Å / Num. unique obs: 6632 / CC1/2: 0.896

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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: 1.7→47.2 Å / SU ML: 0.2111 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 17.3292
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1898 1999 2.92 %
Rwork0.1654 66571 -
obs0.1661 68570 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 27.92 Å2
Refinement stepCycle: LAST / Resolution: 1.7→47.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3825 0 148 518 4491
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01884051
X-RAY DIFFRACTIONf_angle_d1.68435498
X-RAY DIFFRACTIONf_chiral_restr0.104617
X-RAY DIFFRACTIONf_plane_restr0.0135704
X-RAY DIFFRACTIONf_dihedral_angle_d6.4266574
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.740.3051390.28284639X-RAY DIFFRACTION99.79
1.74-1.790.28081400.23894628X-RAY DIFFRACTION100
1.79-1.840.26781400.22154669X-RAY DIFFRACTION100
1.84-1.90.23791410.1934704X-RAY DIFFRACTION100
1.9-1.970.22281390.18214629X-RAY DIFFRACTION100
1.97-2.040.22981410.18644721X-RAY DIFFRACTION100
2.04-2.140.21951410.18984660X-RAY DIFFRACTION100
2.14-2.250.19681420.17214717X-RAY DIFFRACTION100
2.25-2.390.20851410.16434729X-RAY DIFFRACTION100
2.39-2.570.191430.16444755X-RAY DIFFRACTION99.98
2.58-2.830.18541440.16884770X-RAY DIFFRACTION100
2.83-3.240.18611450.16284819X-RAY DIFFRACTION100
3.24-4.090.15581470.14734902X-RAY DIFFRACTION100
4.09-47.20.15871560.13815229X-RAY DIFFRACTION99.94
Refinement TLS params.Method: refined / Origin x: -36.4388821674 Å / Origin y: 35.6519143368 Å / Origin z: -18.804627356 Å
111213212223313233
T0.124146256702 Å20.023417575478 Å2-0.0203398346831 Å2-0.158922795663 Å2-0.0454683750497 Å2--0.129274226289 Å2
L0.172502061345 °20.278760660408 °20.293783298214 °2-0.451343564373 °20.475060460549 °2--0.495541086847 °2
S-0.031666927309 Å °0.0044583445055 Å °0.0445545948399 Å °-0.075406028945 Å °0.0140156296253 Å °0.0302884682948 Å °-0.0787300650181 Å °0.0278057281492 Å °-0.0637670984864 Å °
Refinement TLS groupSelection details: all

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