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- PDB-3uic: Crystal Structure of FabI, an Enoyl Reductase from F. tularensis,... -

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Basic information

Entry
Database: PDB / ID: 3uic
TitleCrystal Structure of FabI, an Enoyl Reductase from F. tularensis, in complex with a Novel and Potent Inhibitor
ComponentsEnoyl-[acyl-carrier-protein] reductase [NADH]
KeywordsOXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR / Rossmann Fold / Enoyl Reductase / NADH Binding / 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-09T / 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: 2.5 Å
AuthorsMehboob, S. / Santarsiero, B.D. / Truong, K. / Johnson, M.E.
CitationJournal: J.Med.Chem. / Year: 2012
Title: Structural and enzymatic analyses reveal the binding mode of a novel series of Francisella tularensis enoyl reductase (FabI) inhibitors.
Authors: Mehboob, S. / Hevener, K.E. / Truong, K. / Boci, T. / Santarsiero, B.D. / Johnson, M.E.
History
DepositionNov 4, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 6, 2012Provider: repository / Type: Initial release
Revision 1.1Feb 6, 2013Group: Database references
Revision 1.2Sep 13, 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]
I: Enoyl-[acyl-carrier-protein] reductase [NADH]
J: Enoyl-[acyl-carrier-protein] reductase [NADH]
K: Enoyl-[acyl-carrier-protein] reductase [NADH]
L: Enoyl-[acyl-carrier-protein] reductase [NADH]
M: Enoyl-[acyl-carrier-protein] reductase [NADH]
N: Enoyl-[acyl-carrier-protein] reductase [NADH]
O: Enoyl-[acyl-carrier-protein] reductase [NADH]
P: Enoyl-[acyl-carrier-protein] reductase [NADH]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)495,60348
Polymers480,10516
Non-polymers15,49832
Water15,511861
1
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)123,90112
Polymers120,0264
Non-polymers3,8758
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19600 Å2
ΔGint-135 kcal/mol
Surface area31990 Å2
MethodPISA
2
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)123,90112
Polymers120,0264
Non-polymers3,8758
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19750 Å2
ΔGint-132 kcal/mol
Surface area32010 Å2
MethodPISA
3
I: Enoyl-[acyl-carrier-protein] reductase [NADH]
J: Enoyl-[acyl-carrier-protein] reductase [NADH]
K: Enoyl-[acyl-carrier-protein] reductase [NADH]
L: Enoyl-[acyl-carrier-protein] reductase [NADH]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)123,90112
Polymers120,0264
Non-polymers3,8758
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19640 Å2
ΔGint-137 kcal/mol
Surface area32010 Å2
MethodPISA
4
M: Enoyl-[acyl-carrier-protein] reductase [NADH]
N: Enoyl-[acyl-carrier-protein] reductase [NADH]
O: Enoyl-[acyl-carrier-protein] reductase [NADH]
P: Enoyl-[acyl-carrier-protein] reductase [NADH]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)123,90112
Polymers120,0264
Non-polymers3,8758
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19700 Å2
ΔGint-136 kcal/mol
Surface area31890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.410, 123.461, 203.330
Angle α, β, γ (deg.)90.00, 90.02, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.342392, 0.939382, -0.018154), (0.93927, 0.341746, -0.03132), (-0.023218, -0.027775, -0.999345)28.11196, -19.54088, 9.29237
3given(-0.999963, 0.006179, 0.005994), (-0.005926, -0.999125, 0.041391), (0.006244, 0.041354, 0.999125)42.83396, 1.33907, -0.10967
4given(0.340855, -0.940055, 0.010658), (-0.939914, -0.340995, -0.016854), (0.019478, -0.004273, -0.999801)14.75562, 21.17805, 8.58004
5given(0.999979, -0.002047, -0.006122), (0.002198, 0.999694, 0.024651), (0.006069, -0.024664, 0.999677)0.99385, -0.51381, -50.85349
6given(-0.343565, 0.939122, 0.003515), (0.938526, 0.343476, -0.034531), (-0.033636, -0.008565, -0.999397)28.51711, -16.88821, 60.38966
7given(-0.999908, 0.004265, 0.012848), (-0.004062, -0.999867, 0.015803), (0.012913, 0.01575, 0.999793)41.50998, -0.29329, -51.09782
8given(0.338886, -0.940746, -0.012381), (-0.940801, -0.338748, -0.011987), (0.007083, 0.015711, -0.999851)14.8527, 20.88298, 59.52029
9given(0.999964, -0.006149, 0.005772), (0.005908, 0.999149, 0.04083), (-0.006018, -0.040794, 0.999149)-0.43212, -2.71647, -101.45449
10given(-0.341373, 0.939871, 0.010354), (0.939741, 0.341504, -0.016168), (-0.018731, 0.004211, -0.999816)28.58145, -17.18802, 111.03803
11given(-1, -9.4E-5, 1.9E-5), (9.4E-5, -1, -0.00035), (1.9E-5, -0.00035, 1)42.68015, -0.3024, -101.65249
12given(0.34264, -0.939291, -0.018173), (-0.93919, -0.342006, -0.030889), (0.022799, 0.027652, -0.999358)15.01928, 23.56123, 109.91725
13given(0.999899, -0.004958, 0.013297), (0.004743, 0.999858, 0.016173), (-0.013375, -0.016108, 0.999781)-2.51462, -1.78557, -152.18405
14given(-0.338523, 0.940908, -0.009769), (0.940927, 0.338409, -0.011607), (-0.007616, -0.013121, -0.999885)30.51215, -17.94481, 161.44713
15given(-0.999981, 0.002644, -0.005537), (-0.002778, -0.9997, 0.024347), (-0.005471, 0.024361, 0.999688)44.18161, -3.22481, -152.22139
16given(0.343249, -0.939238, 0.003576), (-0.938658, -0.343167, -0.034018), (0.033178, 0.008319, -0.999415)13.1812, 26.46787, 160.57813

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Components

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


Mass: 30006.561 Da / Num. of mol.: 16
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Francisella tularensis subsp. tularensis (bacteria)
Strain: Francisella tularensis subsp. TulareNsis Schu4 / Gene: fabI, fabI Coordinates 801554-802336, 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.: 16 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Chemical
ChemComp-09T / 1-(3,4-dichlorobenzyl)-5,6-dimethyl-1H-benzimidazole


Mass: 305.202 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C16H14Cl2N2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 861 / 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: 2.23 Å3/Da / Density % sol: 44.91 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 0.1M sodium acetate, 2.25M ammonium sulfate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 16, 2011
RadiationMonochromator: mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.26→29.7 Å / Num. all: 1252524 / % possible obs: 90 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 31 % / Rmerge(I) obs: 0.107 / Net I/σ(I): 9.4
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
2.26-2.42.20.532.13163.4
2.4-2.5630.423.27195.6

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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: PDB Entry 3NRC

3nrc


Resolution: 2.5→19.99 Å / Cor.coef. Fo:Fc: 0.924 / Cor.coef. Fo:Fc free: 0.886 / SU B: 12.847 / SU ML: 0.277 / Cross valid method: THROUGHOUT / ESU R: 1.328 / ESU R Free: 0.362 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.29213 7281 5 %RANDOM
Rwork0.24122 ---
obs0.24378 137932 99.55 %-
all-145551 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 30.608 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.5→19.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms30847 0 1024 861 32732
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.01932463
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.8162.00143980
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.93754111
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.29724.7911198
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.32155447
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.47815112
X-RAY DIFFRACTIONr_chiral_restr0.1190.25024
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0223732
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: 2.5→2.564 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.362 484 -
Rwork0.315 9783 -
obs--99.27 %

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