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- PDB-4j1n: Crystal structures of FabI from F. tularensis in complex with nov... -

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Basic information

Entry
Database: PDB / ID: 4j1n
TitleCrystal structures of FabI from F. tularensis in complex with novel inhibitors based on the benzimidazole scaffold
ComponentsEnoyl-[acyl-carrier-protein] reductase [NADH]
KeywordsOXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR / Rossmann fold / Reductase / NADH / reduction / OXIDOREDUCTASE-OXIDOREDUCTASE 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-1JN / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Enoyl-[acyl-carrier-protein] reductase [NADH]
Similarity search - Component
Biological speciesFrancisella tularensis subsp. tularensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.45 Å
AuthorsMehboob, S. / Boci, T. / Brubaker, L. / Santarsiero, B.D. / Johnson, M.E.
CitationJournal: Bioorg.Med.Chem.Lett. / Year: 2015
Title: Structural and biological evaluation of a novel series of benzimidazole inhibitors of Francisella tularensis enoyl-ACP reductase (FabI).
Authors: Mehboob, S. / Song, J. / Hevener, K.E. / Su, P.C. / Boci, T. / Brubaker, L. / Truong, L. / Mistry, T. / Deng, J. / Cook, J.L. / Santarsiero, B.D. / Ghosh, A.K. / Johnson, M.E.
History
DepositionFeb 1, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 23, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 12, 2014Group: Structure summary
Revision 1.2Mar 4, 2015Group: Database references
Revision 1.3Mar 18, 2015Group: Database references
Revision 1.4Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)62,0177
Polymers60,0132
Non-polymers2,0045
Water1,13563
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2690 Å2
ΔGint-23 kcal/mol
Surface area21770 Å2
MethodPISA
2
A: Enoyl-[acyl-carrier-protein] reductase [NADH]
B: Enoyl-[acyl-carrier-protein] reductase [NADH]
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)124,03414
Polymers120,0264
Non-polymers4,00710
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area15050 Å2
ΔGint-93 kcal/mol
Surface area33870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.240, 123.320, 50.620
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-407-

HOH

21A-433-

HOH

Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(0.348408, 0.937342, -0.000974), (0.937335, -0.348409, -0.00375), (-0.003854, 0.000394, -0.999992)-0.02402, -0.01581, -8.97053

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Components

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


Mass: 30006.561 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Francisella tularensis subsp. tularensis (bacteria)
Strain: Schu4 / Gene: fabI, FTT_0782 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21
References: UniProt: Q5NGQ3, 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 / Comment: NAD*YM
#3: Chemical ChemComp-1JN / 1-(4-methoxy-3-methylbenzyl)-1,5,6,7-tetrahydroindeno[5,6-d]imidazole


Mass: 292.375 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C19H20N2O
#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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 63 / 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: 2.22 Å3/Da / Density % sol: 44.51 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 0.1M Sodium Acetate, 2.6M Ammonium sulfate, pH4.6, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.978 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 20, 2012
RadiationMonochromator: diamond laue / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 2.45→37 Å / Num. obs: 20080 / % possible obs: 99 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 4.8 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 12.2
Reflection shellResolution: 2.45→2.52 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.675 / Mean I/σ(I) obs: 2.1 / Num. unique all: 1450 / % possible all: 99

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5.6.0117refinement
XDSdata reduction
Aimlessdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3UIC

3uic


Resolution: 2.45→20 Å / Cor.coef. Fo:Fc: 0.92 / Cor.coef. Fo:Fc free: 0.897 / SU B: 13.06 / SU ML: 0.28 / Cross valid method: THROUGHOUT / ESU R: 0.728 / ESU R Free: 0.324 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.28054 1023 5.1 %RANDOM
Rwork0.24225 ---
obs0.24416 20080 99.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 39.321 Å2
Baniso -1Baniso -2Baniso -3
1--3.63 Å20 Å20 Å2
2--2.02 Å20 Å2
3---1.61 Å2
Refinement stepCycle: LAST / Resolution: 2.45→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3856 0 138 63 4057
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0194073
X-RAY DIFFRACTIONr_angle_refined_deg1.0991.9785518
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1025516
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.27324.8150
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.44415681
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.1051514
X-RAY DIFFRACTIONr_chiral_restr0.0750.2630
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.023130
LS refinement shellResolution: 2.455→2.518 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.337 71 -
Rwork0.354 1228 -
obs--99.62 %

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