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- PDB-4j4t: Crystal Structure of FabI from F. tularensis in complex with nove... -

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Basic information

Entry
Database: PDB / ID: 4j4t
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-1JU / 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: 2.34 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 7, 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)248,64236
Polymers240,0528
Non-polymers8,59028
Water15,439857
1
A: Enoyl-[acyl-carrier-protein] reductase [NADH]
B: Enoyl-[acyl-carrier-protein] reductase [NADH]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,31111
Polymers60,0132
Non-polymers2,2989
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5930 Å2
ΔGint-44 kcal/mol
Surface area21020 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)62,1969
Polymers60,0132
Non-polymers2,1837
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5490 Å2
ΔGint-37 kcal/mol
Surface area21130 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)61,9767
Polymers60,0132
Non-polymers1,9635
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5110 Å2
ΔGint-45 kcal/mol
Surface area21040 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)62,1609
Polymers60,0132
Non-polymers2,1477
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5560 Å2
ΔGint-43 kcal/mol
Surface area20990 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)124,50720
Polymers120,0264
Non-polymers4,48116
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area21750 Å2
ΔGint-136 kcal/mol
Surface area31810 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)124,13616
Polymers120,0264
Non-polymers4,10912
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20670 Å2
ΔGint-144 kcal/mol
Surface area32030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.398, 123.349, 202.653
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(0.342167, 0.939639, -7.8E-5), (0.939632, -0.342165, 0.003824), (0.003567, -0.001382, -0.999993)13.57372, -19.47552, 41.68658
3given(-0.34569, -0.938151, -0.019259), (-0.937836, 0.34475, 0.040148), (-0.031025, 0.031941, -0.999008)30.28153, 19.90961, 42.46722
4given(-0.999779, -0.00681, 0.019881), (0.00604, -0.99924, -0.038515), (0.020128, -0.038386, 0.99906)42.95413, 2.05475, -0.31879
5given(-0.999863, -0.001423, 0.016499), (0.001544, -0.999972, 0.007329), (0.016488, 0.007353, 0.999837)43.96798, 0.0884, 50.37334
6given(-0.343128, -0.939212, 0.011972), (-0.938966, 0.343317, 0.021851), (-0.024632, -0.003743, -0.99969)28.76949, 22.10328, -8.38352
7given(0.999983, 0.003486, 0.004742), (-0.003267, 0.998964, -0.045391), (-0.004895, 0.045374, 0.998958)0.03394, 0.24727, 50.74679
8given(0.342195, 0.938994, -0.034531), (0.939587, -0.341601, 0.022031), (0.008891, -0.039984, -0.999161)13.96307, -19.37086, -9.01269

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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, 885 molecules

#2: Chemical
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Chemical
ChemComp-1JU / 1-(1,3-benzodioxol-5-ylmethyl)-5,6,7,8-tetrahydro-1H-naphtho[2,3-d]imidazole


Mass: 306.358 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C19H18N2O2
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#6: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 857 / 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: 44.67 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 4.8
Details: 0.1M Sodium acetate, pH4.8 2.4M Ammonium sulfate, 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: 2.34→20 Å / Num. obs: 90189 / % possible obs: 99 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 13 % / Biso Wilson estimate: 29.4 Å2 / Rmerge(I) obs: 0.138 / Net I/σ(I): 13.5
Reflection shellResolution: 2.34→2.48 Å / Redundancy: 10 % / Rmerge(I) obs: 0.564 / Mean I/σ(I) obs: 4.9 / Num. unique all: 13545 / % possible all: 94.3

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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: 2.34→19.89 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.928 / SU B: 7.223 / SU ML: 0.172 / Cross valid method: THROUGHOUT / ESU R: 0.466 / ESU R Free: 0.256 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.24057 4518 5 %RANDOM
Rwork0.19894 ---
obs0.20102 85571 98.91 %-
all-90198 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.448 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å20 Å2
2--0.03 Å20 Å2
3----0.03 Å2
Refinement stepCycle: LAST / Resolution: 2.34→19.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15494 0 589 857 16940
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.01916438
X-RAY DIFFRACTIONr_angle_refined_deg1.4741.98222271
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.57252080
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.19924.8600
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.141152758
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.1561556
X-RAY DIFFRACTIONr_chiral_restr0.1090.22543
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0212676
LS refinement shellResolution: 2.34→2.399 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.337 279 -
Rwork0.28 5169 -
obs--87.57 %

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