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- PDB-6ahe: Crystal structure of enoyl-ACP reductase from Acinetobacter bauma... -

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Basic information

Entry
Database: PDB / ID: 6ahe
TitleCrystal structure of enoyl-ACP reductase from Acinetobacter baumannii in complex with NAD and AFN-1252
ComponentsEnoyl-[acyl-carrier-protein] reductase [NADH]
KeywordsOXIDOREDUCTASE / Fabi / Acinetobacter baumannii / NAD / AFN-1252 / Inhibitor complex
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 Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-0WE / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / : / 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: 2.29 Å
AuthorsRani, S.T. / Nataraj, V. / Laxminarasimhan, A. / Thomas, A. / Krishnamurthy, N.
CitationJournal: Chem.Biol.Drug Des. / Year: 2020
Title: Ternary complex formation of AFN-1252 with Acinetobacter baumannii FabI and NADH: Crystallographic and biochemical studies.
Authors: Rao, N.K. / Nataraj, V. / Ravi, M. / Panchariya, L. / Palai, K. / Talapati, S.R. / Lakshminarasimhan, A. / Ramachandra, M. / Antony, T.
History
DepositionAug 17, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 21, 2019Provider: repository / Type: Initial release
Revision 1.1Sep 2, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 22, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Enoyl-[acyl-carrier-protein] reductase [NADH]
D: Enoyl-[acyl-carrier-protein] reductase [NADH]
C: Enoyl-[acyl-carrier-protein] reductase [NADH]
B: Enoyl-[acyl-carrier-protein] reductase [NADH]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)118,80612
Polymers114,6434
Non-polymers4,1638
Water2,792155
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14930 Å2
ΔGint-99 kcal/mol
Surface area33920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.529, 89.573, 159.473
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 28660.746 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841 (bacteria)
Strain: ATCC 19606 / AUCC 669 / Gene: NC_009085.1 / Plasmid: pET 28a-AbFabI plasmid / Cell (production host): DE3 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: A0A2J1CZK4, UniProt: D0CAD5*PLUS, enoyl-[acyl-carrier-protein] reductase (NADH)
#2: Chemical
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Chemical
ChemComp-0WE / N-methyl-N-[(3-methyl-1-benzofuran-2-yl)methyl]-3-(7-oxo-5,6,7,8-tetrahydro-1,8-naphthyridin-3-yl)propanamide


Mass: 377.436 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C22H23N3O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 155 / 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: 2.48 Å3/Da / Density % sol: 50.35 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 6.5 / Details: 0.1M MES pH 6.5, 100mM NaCl, 5% PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 15, 2018
RadiationMonochromator: Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.29→87.67 Å / Num. obs: 51845 / % possible obs: 99.4 % / Redundancy: 6.5 % / Rmerge(I) obs: 0.059 / Net I/σ(I): 11.2
Reflection shellResolution: 2.29→2.36 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.357 / Mean I/σ(I) obs: 2 / Num. unique obs: 4194

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
XDSdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4zju

4zju


Resolution: 2.29→79.74 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.933 / SU B: 10.723 / SU ML: 0.247 / Cross valid method: THROUGHOUT / ESU R: 0.345 / ESU R Free: 0.257 / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.26764 2527 4.9 %RANDOM
Rwork0.2036 ---
obs0.20676 49249 99.41 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 57.115 Å2
Baniso -1Baniso -2Baniso -3
1--0.08 Å2-0 Å20 Å2
2--0.06 Å2-0 Å2
3---0.02 Å2
Refinement stepCycle: 1 / Resolution: 2.29→79.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7768 0 288 155 8211
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0198225
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.861211177
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.07351036
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.02123.78328
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.528151265
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.4831548
X-RAY DIFFRACTIONr_chiral_restr0.1160.21248
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0216220
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it4.3595.5244156
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it6.2018.2645188
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it5.3965.8734069
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined12.09877.72613132
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.29→2.349 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.353 170 -
Rwork0.334 3393 -
obs--93.08 %

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