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

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Basic information

Entry
Database: PDB / ID: 7umy
TitleCrystal structure of Acinetobacter baumannii 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]
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-NUC / 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: 2.74 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
Water39622
1
A: Enoyl-[acyl-carrier-protein] reductase [NADH]
C: 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)120,38412
Polymers116,1124
Non-polymers4,2728
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Enoyl-[acyl-carrier-protein] reductase [NADH]
hetero molecules

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

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

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
crystal symmetry operation2_556-x,y,-z+11
crystal symmetry operation1_556x,y,z+11
crystal symmetry operation2_555-x,y,-z1
Unit cell
Length a, b, c (Å)256.215, 79.137, 89.425
Angle α, β, γ (deg.)90.000, 110.297, 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 4 through 9 or (resid 10...
d_2ens_1(chain "B" and (resid 4 through 18 or (resid 19...
d_3ens_1(chain "C" and (resid 4 through 11 or (resid 12...
d_4ens_1(chain "D" and (resid 4 through 10 or (resid 11...
d_5ens_1(chain "E" and (resid 4 through 9 or (resid 10...
d_6ens_1(chain "F" and (resid 4 through 9 or (resid 10...

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1GLYALAA1 - 65
d_12ens_1ASPASPA67 - 85
d_13ens_1HISGLYA89 - 178
d_14ens_1GLYSERA181 - 259
d_21ens_1GLYALAD1 - 65
d_22ens_1ASPSERD67 - 254
d_31ens_1GLYALAG2 - 66
d_32ens_1ASPASPG68 - 86
d_33ens_1HISGLYG90 - 179
d_34ens_1GLYSERG182 - 260
d_41ens_1GLYASPJ1 - 84
d_42ens_1HISGLYJ88 - 177
d_43ens_1GLYSERJ180 - 258
d_51ens_1GLYALAM2 - 66
d_52ens_1ASPASPM68 - 86
d_53ens_1HISGLYM90 - 179
d_54ens_1GLYSERM182 - 260
d_61ens_1GLYALAP2 - 66
d_62ens_1ASPASPP68 - 86
d_63ens_1HISGLYP90 - 179
d_64ens_1GLYSERP182 - 260

NCS oper:
IDCodeMatrixVector
1given(-0.987792800249, 0.0945137241324, -0.123824632958), (0.0899349461393, 0.995058599837, 0.0420724179746), (0.127189186802, 0.0304226698686, -0.991411807434)25.9926273103, 36.1900613955, 50.7615943352
2given(-0.988664127556, 0.150137927902, 0.00135848785959), (0.149733079249, 0.98524846063, 0.0828581667909), (0.0111017053993, 0.0821223077516, -0.996560424012)78.6887953824, -7.06602255622, 27.5301967671
3given(-0.781437114015, 0.0588927670753, -0.621198582441), (-0.0555740071685, -0.9981485074, -0.0247201719562), (-0.621504277192, 0.0152052346423, 0.783263196041)54.8247540097, -4.83420110682, -28.4090245426
4given(-0.702273060479, 0.00336314377249, -0.71189973858), (0.0137827040783, -0.99973718622, -0.0183192673911), (-0.711774251848, -0.0226770314067, 0.702042140226)73.6504478092, -47.6271758621, 30.1267033532
5given(0.693437923073, -0.146692588936, 0.705425496559), (-0.14031308366, -0.987804684597, -0.0674843955399), (0.70672207083, -0.0521841876318, -0.705564118393)-1.15206360179, -40.954429973, -5.70111721244

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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-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 6 / 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.: 6 / Source method: obtained synthetically / Formula: C23H24N4O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 22 / 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: 2.44 Å3/Da / Density % sol: 49.61 %
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: 2.74→28.92 Å / Num. obs: 43821 / % possible obs: 98.5 % / Redundancy: 3 % / CC1/2: 0.999 / Net I/σ(I): 8.4
Reflection shellResolution: 2.74→2.83 Å / Num. unique obs: 4057 / CC1/2: 0.62

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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: 2.74→28.92 Å / Cross valid method: FREE R-VALUE / σ(F): 94.05 / Phase error: 40.4536
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2956 2002 4.58 %
Rwork0.2556 41734 -
obs0.2603 43736 98.37 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 94.48 Å2
Refinement stepCycle: LAST / Resolution: 2.74→28.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11455 0 444 22 11921
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006712147
X-RAY DIFFRACTIONf_angle_d1.358916524
X-RAY DIFFRACTIONf_chiral_restr0.11751864
X-RAY DIFFRACTIONf_plane_restr0.01522112
X-RAY DIFFRACTIONf_dihedral_angle_d9.27231712
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AX-RAY DIFFRACTIONTorsion NCS1.00190826455
ens_1d_3AX-RAY DIFFRACTIONTorsion NCS0.797575586724
ens_1d_4AX-RAY DIFFRACTIONTorsion NCS0.918696533092
ens_1d_5AX-RAY DIFFRACTIONTorsion NCS0.826263718498
ens_1d_6AX-RAY DIFFRACTIONTorsion NCS0.836697689356
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.74-2.810.33061240.32112501X-RAY DIFFRACTION79.73
2.81-2.880.30461420.32363009X-RAY DIFFRACTION95.46
2.88-2.970.3641420.31843007X-RAY DIFFRACTION95.49
2.97-3.060.29351400.32513035X-RAY DIFFRACTION95.56
3.06-3.170.31451400.32573009X-RAY DIFFRACTION95.55
3.17-3.30.36781480.31763029X-RAY DIFFRACTION95.25
3.3-3.450.33111430.3152983X-RAY DIFFRACTION95.3
3.45-3.630.35651440.31653022X-RAY DIFFRACTION94.53
3.63-3.860.33811430.3052935X-RAY DIFFRACTION93.47
3.86-4.150.29571420.26813015X-RAY DIFFRACTION94.66
4.15-4.570.28881420.23692988X-RAY DIFFRACTION94.41
4.57-5.230.24921450.22583043X-RAY DIFFRACTION95.09
5.23-6.570.28921470.23733057X-RAY DIFFRACTION95.17
6.58-28.920.26461480.19583113X-RAY DIFFRACTION94.68
Refinement TLS params.Method: refined / Origin x: 30.275703086 Å / Origin y: -10.7899135248 Å / Origin z: 9.91836041613 Å
111213212223313233
T0.596992679759 Å2-0.094698971392 Å2-0.0582315988116 Å2-0.727269510808 Å20.092848917427 Å2--0.451389316948 Å2
L0.549570893681 °2-0.0530571279788 °2-0.164803874848 °2-0.665414731443 °20.16836030828 °2--0.523870672356 °2
S-0.139101520951 Å °-0.140346223959 Å °-0.175785514091 Å °-0.0356414130064 Å °-0.0503852388138 Å °0.0594560206525 Å °-0.134444946238 Å °0.142689573985 Å °0.181627924187 Å °
Refinement TLS groupSelection details: all

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