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- PDB-4j3f: Crystal Structure of FabI from F. tularensis in complex with nove... -

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Basic information

Entry
Database: PDB / ID: 4j3f
TitleCrystal Structure 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-1JT / ACETATE ION / 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: 1.85 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 5, 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]
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]
G: Enoyl-[acyl-carrier-protein] reductase [NADH]
H: Enoyl-[acyl-carrier-protein] reductase [NADH]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)248,89242
Polymers240,0528
Non-polymers8,83934
Water23,8521324
1
A: Enoyl-[acyl-carrier-protein] reductase [NADH]
B: Enoyl-[acyl-carrier-protein] reductase [NADH]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,46213
Polymers60,0132
Non-polymers2,44911
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6340 Å2
ΔGint-49 kcal/mol
Surface area20700 Å2
MethodPISA
2
C: Enoyl-[acyl-carrier-protein] reductase [NADH]
D: Enoyl-[acyl-carrier-protein] reductase [NADH]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,0358
Polymers60,0132
Non-polymers2,0226
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5280 Å2
ΔGint-47 kcal/mol
Surface area20920 Å2
MethodPISA
3
E: Enoyl-[acyl-carrier-protein] reductase [NADH]
F: Enoyl-[acyl-carrier-protein] reductase [NADH]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,27811
Polymers60,0132
Non-polymers2,2659
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5690 Å2
ΔGint-49 kcal/mol
Surface area20890 Å2
MethodPISA
4
G: Enoyl-[acyl-carrier-protein] reductase [NADH]
H: Enoyl-[acyl-carrier-protein] reductase [NADH]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,11710
Polymers60,0132
Non-polymers2,1048
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5740 Å2
ΔGint-53 kcal/mol
Surface area20880 Å2
MethodPISA
5
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)124,49721
Polymers120,0264
Non-polymers4,47117
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area21660 Å2
ΔGint-148 kcal/mol
Surface area31580 Å2
MethodPISA
6
E: Enoyl-[acyl-carrier-protein] reductase [NADH]
F: Enoyl-[acyl-carrier-protein] reductase [NADH]
G: Enoyl-[acyl-carrier-protein] reductase [NADH]
H: Enoyl-[acyl-carrier-protein] reductase [NADH]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)124,39521
Polymers120,0264
Non-polymers4,36917
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area21450 Å2
ΔGint-155 kcal/mol
Surface area31760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.421, 123.360, 202.717
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(0.34204, 0.939683, -0.002128), (0.939683, -0.342033, 0.003184), (0.002264, -0.003089, -0.999993)13.60851, -19.46624, 41.7616
3given(-0.3451, -0.938354, -0.019952), (-0.938008, 0.344084, 0.041792), (-0.032351, 0.033138, -0.998927)30.30754, 19.90913, 42.5377
4given(-0.999722, -0.007077, 0.0225), (0.006199, -0.999224, -0.038888), (0.022758, -0.038738, 0.99899)42.92012, 2.10273, -0.39647
5given(-0.999826, -0.001635, 0.018582), (0.001773, -0.999971, 0.007403), (0.01857, 0.007434, 0.9998)44.05324, 0.08841, 50.35525
6given(-0.342916, -0.939302, 0.010985), (-0.938992, 0.343086, 0.024212), (-0.026512, -0.002012, -0.999646)28.73573, 22.20491, -8.31707
7given(0.99998, 0.004254, 0.004639), (-0.004038, 0.998949, -0.045654), (-0.004829, 0.045634, 0.998947)0.02285, 0.28074, 50.75618
8given(0.342073, 0.938985, -0.03597), (0.939644, -0.341509, 0.021016), (0.00745, -0.040988, -0.999132)13.94439, -19.42174, -8.93781

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Components

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Protein , 1 types, 8 molecules ABCDEFGH

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


Mass: 30006.561 Da / Num. of mol.: 8
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)

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Non-polymers , 6 types, 1358 molecules

#2: Chemical
ChemComp-1JT / 1-(4-methoxy-3-methylbenzyl)-5,6,7,8-tetrahydro-1H-naphtho[2,3-d]imidazole


Mass: 306.401 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C20H22N2O
#3: Chemical
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 8 / 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.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H3O2
#6: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Na
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1324 / 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: 44.71 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 4.8
Details: 0.15M Sodium acetate, 2.5M ammonium sulfate, pH 4.8, 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: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 1.85→20 Å / Num. obs: 178885 / % possible obs: 99 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 13 % / Rmerge(I) obs: 0.066 / Net I/σ(I): 29.5
Reflection shellResolution: 1.85→1.96 Å / Redundancy: 1.1 % / Rmerge(I) obs: 0.195 / Mean I/σ(I) obs: 9.85 / % possible all: 90.5

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Processing

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

3uic


Resolution: 1.85→19.79 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.953 / SU B: 2.116 / SU ML: 0.066 / Cross valid method: THROUGHOUT / ESU R: 0.124 / ESU R Free: 0.111 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.18221 8974 5 %RANDOM
Rwork0.15582 ---
obs0.15717 169807 98.39 %-
all-178885 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 13.728 Å2
Baniso -1Baniso -2Baniso -3
1--0.04 Å20 Å20 Å2
2--0.02 Å20 Å2
3---0.02 Å2
Refinement stepCycle: LAST / Resolution: 1.85→19.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15496 0 605 1324 17425
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.01916529
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3631.98522395
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.15652106
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.69424.809601
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.234152811
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.6261556
X-RAY DIFFRACTIONr_chiral_restr0.0980.22557
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0212684
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.853→1.901 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.208 572 -
Rwork0.166 10219 -
obs--84.42 %

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