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- PDB-9l5x: Crystal structure of Klebsiella pneumoniae Enoyl-Acyl Carrier Pro... -

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Basic information

Entry
Database: PDB / ID: 9l5x
TitleCrystal structure of Klebsiella pneumoniae Enoyl-Acyl Carrier Protein Reductase (FabI) in complex with Triclosan
ComponentsEnoyl-[acyl-carrier-protein] reductase [NADH]
KeywordsOXIDOREDUCTASE / Enoyl Reductase / Klebsiella pneumoniae / FabI / Triclosan / Inhbibitor / Complex
Function / homology
Function and homology information


biotin biosynthetic process / enoyl-[acyl-carrier-protein] reductase (NADH) / enoyl-[acyl-carrier-protein] reductase (NADH) activity / fatty acid biosynthetic process
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 / TRICLOSAN / Enoyl-[acyl-carrier-protein] reductase [NADH]
Similarity search - Component
Biological speciesKlebsiella pneumoniae subsp. pneumoniae 12-3578 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.09 Å
AuthorsBiswas, S. / Patra, A. / Kushwaha, G.S. / Suar, M.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Crystal structure of Klebsiella pneumoniae Enoyl-Acyl Carrier Protein Reductase (FabI) in complex with Triclosan
Authors: Biswas, S. / Patra, A. / Kushwaha, G.S. / Suar, M.
History
DepositionDec 23, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 15, 2025Provider: repository / Type: Initial release

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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]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,95115
Polymers112,8894
Non-polymers4,06211
Water13,493749
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, Tetramer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area22620 Å2
ΔGint-211 kcal/mol
Surface area30330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.572, 124.712, 70.743
Angle α, β, γ (deg.)90.00, 110.38, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Enoyl-[acyl-carrier-protein] reductase [NADH] / Enoyl ACP Reductase (FabI)


Mass: 28222.311 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae subsp. pneumoniae 12-3578 (bacteria)
Strain: MTCC109
Gene: fabI, E9161_16145, GLO21_010850, GLO21_17500, NCTC9504_03879
Production host: Escherichia coli BL21 (bacteria)
References: UniProt: A0A1Y0Q1M7, enoyl-[acyl-carrier-protein] reductase (NADH)

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Non-polymers , 6 types, 760 molecules

#2: Chemical
ChemComp-TCL / TRICLOSAN


Mass: 289.542 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C12H7Cl3O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 749 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationN

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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: 2.3 Å3/Da / Density % sol: 46.79 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.7
Details: 0.1M Sodium Citrate pH 5.7, 0.1M Ammonium Sulphate, 20% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM07 / Wavelength: 0.97951 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 23, 2023
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97951 Å / Relative weight: 1
ReflectionResolution: 2.09→66.32 Å / Num. obs: 57229 / % possible obs: 95.2 % / Redundancy: 6.7 % / CC1/2: 0.997 / Rmerge(I) obs: 0.119 / Rpim(I) all: 0.075 / Rrim(I) all: 0.141 / Χ2: 0.93 / Net I/σ(I): 10.6
Reflection shellResolution: 2.09→2.2 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.663 / Mean I/σ(I) obs: 2.4 / Num. unique obs: 8029 / CC1/2: 0.884 / Rpim(I) all: 0.445 / Rrim(I) all: 0.779 / Χ2: 0.86 / % possible all: 92.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
autoPROCdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.09→66.32 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.937 / SU B: 7.753 / SU ML: 0.184 / Cross valid method: THROUGHOUT / ESU R: 0.242 / ESU R Free: 0.203 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23389 2782 4.9 %RANDOM
Rwork0.16607 ---
obs0.16936 54418 95.12 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 38.805 Å2
Baniso -1Baniso -2Baniso -3
1--0.62 Å20 Å23.7 Å2
2---4.89 Å2-0 Å2
3---2.16 Å2
Refinement stepCycle: 1 / Resolution: 2.09→66.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7673 0 259 749 8681
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0138192
X-RAY DIFFRACTIONr_bond_other_d0.0010.0157692
X-RAY DIFFRACTIONr_angle_refined_deg1.4941.63411142
X-RAY DIFFRACTIONr_angle_other_deg1.2931.57517683
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.50351060
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.57322.252373
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.4151289
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.6931547
X-RAY DIFFRACTIONr_chiral_restr0.070.21104
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.029401
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021841
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_it2.533.9564171
X-RAY DIFFRACTIONr_mcbond_other2.5233.9564170
X-RAY DIFFRACTIONr_mcangle_it3.4985.9265218
X-RAY DIFFRACTIONr_mcangle_other3.55.9275219
X-RAY DIFFRACTIONr_scbond_it3.0614.2694021
X-RAY DIFFRACTIONr_scbond_other3.064.2694022
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.5086.2855913
X-RAY DIFFRACTIONr_long_range_B_refined6.42148.9569608
X-RAY DIFFRACTIONr_long_range_B_other6.40548.9029579
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.09→2.144 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.355 203 -
Rwork0.314 3741 -
obs--88.43 %

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