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- PDB-5bns: E. coli Fabh with small molecule inhibitor 2 -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 5bns
TitleE. coli Fabh with small molecule inhibitor 2
Components3-oxoacyl-[acyl-carrier-protein] synthase 3
KeywordsTransferase/Transferase Inhibitor / Fabh / Fatty acid synthesis / anti-bacterials / Transferase-Transferase Inhibitor complex
Function / homology
Function and homology information


beta-ketoacyl-[acyl-carrier-protein] synthase III / beta-ketoacyl-acyl-carrier-protein synthase III activity / 3-oxoacyl-[acyl-carrier-protein] synthase activity / fatty acid metabolic process / fatty acid biosynthetic process / cytosol
Similarity search - Function
3-oxoacyl-[acyl-carrier-protein] synthase 3 / 3-Oxoacyl-[acyl-carrier-protein (ACP)] synthase III / 3-Oxoacyl-[acyl-carrier-protein (ACP)] synthase III / 3-Oxoacyl-[acyl-carrier-protein (ACP)] synthase III, C-terminal / 3-Oxoacyl-[acyl-carrier-protein (ACP)] synthase III C terminal / Thiolase/Chalcone synthase / Peroxisomal Thiolase; Chain A, domain 1 / Thiolase-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-4VM / Beta-ketoacyl-[acyl-carrier-protein] synthase III
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / Resolution: 2.2 Å
AuthorsKazmirski, S.L. / McKinney, D.C.
CitationJournal: Acs Infect Dis. / Year: 2016
Title: Antibacterial FabH Inhibitors with Mode of Action Validated in Haemophilus influenzae by in Vitro Resistance Mutation Mapping.
Authors: McKinney, D.C. / Eyermann, C.J. / Gu, R.F. / Hu, J. / Kazmirski, S.L. / Lahiri, S.D. / McKenzie, A.R. / Shapiro, A.B. / Breault, G.
History
DepositionMay 26, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 18, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 28, 2016Group: Database references
Revision 1.2Mar 6, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 3-oxoacyl-[acyl-carrier-protein] synthase 3
B: 3-oxoacyl-[acyl-carrier-protein] synthase 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,0354
Polymers67,0942
Non-polymers9412
Water10,863603
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4590 Å2
ΔGint-29 kcal/mol
Surface area21510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.907, 66.878, 162.011
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein 3-oxoacyl-[acyl-carrier-protein] synthase 3 / 3-oxoacyl-[acyl-carrier-protein] synthase III / Beta-ketoacyl-ACP synthase III / KAS III / EcFabH


Mass: 33547.027 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: fabH, b1091, JW1077 / Production host: Escherichia coli (E. coli)
References: UniProt: P0A6R0, beta-ketoacyl-[acyl-carrier-protein] synthase III
#2: Chemical ChemComp-4VM / 1-{5-[2-fluoro-5-(hydroxymethyl)phenyl]pyridin-2-yl}-N-(quinolin-6-ylmethyl)piperidine-4-carboxamide


Mass: 470.538 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C28H27FN4O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 603 / 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: 2.58 Å3/Da / Density % sol: 52.33 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: 14% PEG 4000, 0.1 M magnesium chloride, 0.1 m Tris / PH range: 7.9-8.4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.54 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Apr 21, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.2→31.95 Å / Num. obs: 34647 / % possible obs: 96.1 % / Redundancy: 2.78 % / Rsym value: 0.122 / Net I/σ(I): 5.5
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 2.28 % / Rmerge(I) obs: 0.455 / Mean I/σ(I) obs: 1.4 / % possible all: 94.3

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
BUSTER2.11.6refinement
PDB_EXTRACT3.15data extraction
AMoREphasing
RefinementResolution: 2.2→31.34 Å / Cor.coef. Fo:Fc: 0.9389 / Cor.coef. Fo:Fc free: 0.9034 / SU R Cruickshank DPI: 0.321 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.385 / SU Rfree Blow DPI: 0.264 / SU Rfree Cruickshank DPI: 0.252
RfactorNum. reflection% reflectionSelection details
Rfree0.2871 1731 5 %RANDOM
Rwork0.2252 ---
obs0.2283 34633 96.05 %-
Displacement parametersBiso max: 115.45 Å2 / Biso mean: 40.11 Å2 / Biso min: 17.7 Å2
Baniso -1Baniso -2Baniso -3
1--3.1802 Å20 Å20 Å2
2---2.0998 Å20 Å2
3---5.28 Å2
Refine analyzeLuzzati coordinate error obs: 0.313 Å
Refinement stepCycle: final / Resolution: 2.2→31.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4702 0 70 603 5375
Biso mean--38.85 49.72 -
Num. residues----634
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1645SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes113HARMONIC2
X-RAY DIFFRACTIONt_gen_planes780HARMONIC5
X-RAY DIFFRACTIONt_it4865HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion673SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact6171SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d4865HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg6625HARMONIC21.12
X-RAY DIFFRACTIONt_omega_torsion3.25
X-RAY DIFFRACTIONt_other_torsion17.62
LS refinement shellResolution: 2.2→2.27 Å / Total num. of bins used: 17
RfactorNum. reflection% reflection
Rfree0.2379 123 4.26 %
Rwork0.2171 2765 -
all0.2179 2888 -
obs--94.35 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.37330.1181-0.04740.6655-0.13390.47310.0216-0.0348-0.00050.0321-0.03650.01780.0428-0.01140.0148-0.06770.0127-0.0078-0.0253-0.0009-0.06828.970118.588169.4272
20.44970.0690.15820.5933-0.20680.98020.00130.07620.1010.0105-0.0335-0.0267-0.08550.10550.0323-0.09820.0102-0.0035-0.01480.0303-0.060618.908939.046650.4031
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|1 - A|317 }A1 - 317
2X-RAY DIFFRACTION2{ B|1 - B|317 }B1 - 317

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