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- PDB-7umx: Crystal structure of Acinetobacter baumannii FabI in complex with... -

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Basic information

Entry
Database: PDB / ID: 7umx
TitleCrystal structure of Acinetobacter baumannii 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]
KeywordsANTIBIOTIC / enoyl reductase / FabI / antimicrobial resistance
Function / homology
Function and homology information


enoyl-[acyl-carrier-protein] reductase (NADH) / enoyl-[acyl-carrier-protein] reductase (NADH) activity / fatty acid biosynthetic process / nucleotide binding
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]
Similarity search - Component
Biological speciesAcinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.39 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 8, 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.gene_src_strain / _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]
B: Enoyl-[acyl-carrier-protein] reductase [NADH]
C: Enoyl-[acyl-carrier-protein] reductase [NADH]
D: Enoyl-[acyl-carrier-protein] reductase [NADH]
E: Enoyl-[acyl-carrier-protein] reductase [NADH]
F: Enoyl-[acyl-carrier-protein] reductase [NADH]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)180,57618
Polymers174,1696
Non-polymers6,40712
Water3,045169
1
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)120,38412
Polymers116,1124
Non-polymers4,2728
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
E: Enoyl-[acyl-carrier-protein] reductase [NADH]
hetero molecules

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

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

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


Theoretical massNumber of molelcules
Total (without water)120,38412
Polymers116,1124
Non-polymers4,2728
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_554-x,y,-z-11
crystal symmetry operation1_554x,y,z-11
crystal symmetry operation2_555-x,y,-z1
Unit cell
Length a, b, c (Å)255.120, 79.250, 89.900
Angle α, β, γ (deg.)90.000, 110.296, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 3 through 197 or (resid 198...
d_2ens_1(chain "B" and (resid 3 through 18 or (resid 19...
d_3ens_1(chain "C" and (resid 3 through 18 or (resid 19...
d_4ens_1(chain "D" and (resid 3 through 18 or (resid 19...
d_5ens_1(chain "E" and (resid 3 through 18 or (resid 19...
d_6ens_1(chain "F" and (resid 3 through 18 or (resid 19...

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1GLNTHRA1 - 254
d_12ens_1METSERA257 - 260
d_21ens_1GLNTHRD1 - 254
d_22ens_1METSERD257 - 260
d_31ens_1GLNTHRG1 - 254
d_32ens_1METSERG257 - 260
d_41ens_1GLNTHRJ1 - 254
d_42ens_1METSERJ257 - 260
d_51ens_1GLNTHRM1 - 254
d_52ens_1METSERM257 - 260
d_61ens_1GLNSERP1 - 258

NCS oper:
IDCodeMatrixVector
1given(-0.807474872754, -0.00189966719175, -0.589898907556), (0.0129434946371, -0.999811121986, -0.0144978032493), (-0.58975994762, -0.0193419651804, 0.807346946836)75.364801134, 42.8411700874, 24.7881205617
2given(0.795532162046, 0.160745724118, 0.584199787169), (0.159331618407, -0.985732846424, 0.0542603985955), (0.58458704615, 0.0499156053548, -0.809794058891)-4.77071098491, 36.164490674, 4.40550141605
3given(-0.98648994715, -0.163750459335, 0.004834381058), (-0.163820968061, 0.986149665643, -0.0259138452633), (-0.000524019198947, -0.0263557208291, -0.99965249031)76.4636534725, 6.7652337342, 30.2702930432
4given(0.993165421557, 0.048896082032, -0.105979330931), (-0.0474652888655, 0.998745012544, 0.0159826866431), (0.106627818957, -0.0108431121611, 0.994239878069)-20.1121453085, -39.0667602286, -60.0174824468
5given(0.73443328402, 0.11333728227, 0.669150515035), (0.136072541072, -0.990527572034, 0.0184226112753), (0.664900003677, 0.0775228320415, -0.742898509638)-54.8433066008, -2.89782601704, 27.727914754

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Components

#1: Protein
Enoyl-[acyl-carrier-protein] reductase [NADH]


Mass: 29028.088 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841 (bacteria)
Strain: 19606 / Gene: fabI / Production host: Escherichia coli (E. coli)
References: UniProt: D0CAD5, enoyl-[acyl-carrier-protein] reductase (NADH)
#2: 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.: 6 / Source method: obtained synthetically / Formula: C23H24N4O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 169 / 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: 2.45 Å3/Da / Density % sol: 49.73 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 100 mM HEPES pH 6.5-7.5 20% PEG 4K 15%-20% 2-propanolol

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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: Aug 6, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.39→44.95 Å / Num. obs: 65755 / % possible obs: 98.68 % / Redundancy: 2.5 % / CC1/2: 0.99 / Net I/σ(I): 11.39
Reflection shellResolution: 2.39→2.47 Å / Num. unique obs: 6497 / CC1/2: 0.83

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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: 6AHE

6ahe


Resolution: 2.39→44.95 Å / Cross valid method: FREE R-VALUE / σ(F): 2.13 / Phase error: 27.3448
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.251 2030 3.09 %
Rwork0.2076 63725 -
obs0.213 65755 98.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 45.31 Å2
Refinement stepCycle: LAST / Resolution: 2.39→44.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11611 0 444 169 12224
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.002712312
X-RAY DIFFRACTIONf_angle_d0.655316736
X-RAY DIFFRACTIONf_chiral_restr0.03991875
X-RAY DIFFRACTIONf_plane_restr0.00482136
X-RAY DIFFRACTIONf_dihedral_angle_d6.60961729
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AX-RAY DIFFRACTIONTorsion NCS0.652840930354
ens_1d_3AX-RAY DIFFRACTIONTorsion NCS0.713601350098
ens_1d_4AX-RAY DIFFRACTIONTorsion NCS0.687871789064
ens_1d_5AX-RAY DIFFRACTIONTorsion NCS0.755144700156
ens_1d_6AX-RAY DIFFRACTIONTorsion NCS0.761715262806
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.39-2.450.3461420.29724435X-RAY DIFFRACTION94.93
2.45-2.520.30161440.27514595X-RAY DIFFRACTION96.94
2.52-2.590.28431460.27574578X-RAY DIFFRACTION96.87
2.59-2.680.25961410.28134614X-RAY DIFFRACTION96.89
2.68-2.770.2961390.26394577X-RAY DIFFRACTION97.01
2.77-2.880.30731470.26094585X-RAY DIFFRACTION96.75
2.88-3.010.29811420.24324584X-RAY DIFFRACTION96.81
3.01-3.170.30691440.2444595X-RAY DIFFRACTION96.17
3.17-3.370.25361440.23134521X-RAY DIFFRACTION95.78
3.37-3.630.27211430.21714559X-RAY DIFFRACTION95.08
3.63-40.24711340.19274416X-RAY DIFFRACTION93.18
4-4.580.23741400.17054463X-RAY DIFFRACTION93.54
4.58-5.760.20381470.16634559X-RAY DIFFRACTION94.76
5.76-44.950.22151510.18424670X-RAY DIFFRACTION95.02
Refinement TLS params.Method: refined / Origin x: 29.2002283689 Å / Origin y: 8.363654185 Å / Origin z: 12.0847402076 Å
111213212223313233
T0.255104829288 Å20.0218403181852 Å20.0688835344866 Å2-0.288508370898 Å20.0515726985957 Å2--0.295154048958 Å2
L0.124266293883 °2-0.0172246432172 °20.0111678782436 °2-0.404945043324 °20.107176086446 °2--0.278956367846 °2
S-0.0242643352099 Å °-0.0121453458861 Å °-0.0360516772176 Å °-0.00926955697371 Å °-0.00266634388898 Å °0.0469614223527 Å °-0.0472953795036 Å °0.0642603736478 Å °0.044803022507 Å °
Refinement TLS groupSelection details: all

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