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- PDB-4z8d: Antibacterial FabH Inhibitors with Validated Mode of Action in Ha... -

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Basic information

Entry
Database: PDB / ID: 4z8d
TitleAntibacterial FabH Inhibitors with Validated Mode of Action in Haemophilus Influenzae by in vitro resistance mutation mapping
Components3-oxoacyl-[acyl-carrier-protein] synthase 3
KeywordsTransferase/Transferase inhibitor / Beta-ketoacyl-(acyl-carrier-protein) synthase III / carbamate / structure based drug design / fatty acid biosynthesis / 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 / cytoplasm
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-4LB / Beta-ketoacyl-[acyl-carrier-protein] synthase III / 3-oxoacyl-[acyl-carrier-protein] synthase 3
Similarity search - Component
Biological speciesEscherichia coli O157:H7 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2 Å
AuthorsLahiri, S.D.
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
DepositionApr 8, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 4, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 28, 2016Group: Data collection / 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)67,9386
Polymers67,0942
Non-polymers8444
Water5,585310
1
A: 3-oxoacyl-[acyl-carrier-protein] synthase 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,9693
Polymers33,5471
Non-polymers4222
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: 3-oxoacyl-[acyl-carrier-protein] synthase 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,9693
Polymers33,5471
Non-polymers4222
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4440 Å2
ΔGint-27 kcal/mol
Surface area21710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.370, 79.496, 120.530
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


Mass: 33547.027 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli O157:H7 (bacteria) / Gene: fabH, Z1730, ECs1469 / Production host: Escherichia coli (E. coli)
References: UniProt: P0A6R2, UniProt: P0A6R0*PLUS, beta-ketoacyl-[acyl-carrier-protein] synthase III
#2: Chemical ChemComp-4LB / trans-4-[({[(2-chlorobenzyl)oxy]carbonyl}amino)methyl]cyclohexanecarboxylic acid


Mass: 325.787 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H20ClNO4
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 310 / 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: 2.26 Å3/Da / Density % sol: 45.63 %
Crystal growTemperature: 283 K / Method: vapor diffusion, hanging drop
Details: 25 mM Tris pH 7.5, 150 mM NaCl, 10% Glycerol, 1mM TCEP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X26C / Wavelength: 0.987 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jan 9, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 2→28.05 Å / Num. obs: 34795 / % possible obs: 84.1 % / Redundancy: 3.4 % / Net I/σ(I): 14.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
PDB_EXTRACT3.15data extraction
SCALAdata scaling
AMoREphasing
RefinementResolution: 2→25.74 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.902 / SU B: 3.729 / SU ML: 0.105 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.217 / ESU R Free: 0.183 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2151 1753 5 %RANDOM
Rwork0.1578 ---
obs0.1607 33013 83.02 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 64.39 Å2 / Biso mean: 15.267 Å2 / Biso min: 3.58 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å2-0 Å2-0 Å2
2---0.03 Å20 Å2
3---0.04 Å2
Refinement stepCycle: final / Resolution: 2→25.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4702 0 54 310 5066
Biso mean--26.93 22.69 -
Num. residues----634
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0194876
X-RAY DIFFRACTIONr_bond_other_d0.0020.024624
X-RAY DIFFRACTIONr_angle_refined_deg1.7091.9626639
X-RAY DIFFRACTIONr_angle_other_deg1.03310620
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6825640
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.53924.381194
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.06815771
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.421528
X-RAY DIFFRACTIONr_chiral_restr0.1010.2784
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.025590
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021050
X-RAY DIFFRACTIONr_mcbond_it1.1561.3592554
X-RAY DIFFRACTIONr_mcbond_other1.1541.3592553
X-RAY DIFFRACTIONr_mcangle_it1.7482.033196
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.264 55 -
Rwork0.186 1069 -
all-1124 -
obs--37.28 %

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