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Basic information

Entry
Database: PDB / ID: 2foi
TitleSynthesis, Biological Activity, and X-Ray Crystal Structural Analysis of Diaryl Ether Inhibitors of Malarial Enoyl ACP Reductase.
Components(enoyl-acyl carrier reductase) x 2
KeywordsOXIDOREDUCTASE / enoyl reductase / rossmann fold
Function / homology
Function and homology information


apicoplast / enoyl-[acyl-carrier-protein] reductase activity (NAD(P)H) / 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 / Enoyl-[acyl-carrier-protein] reductase (NADH) / Enoyl-(Acyl carrier protein) reductase / Helicase, Ruva Protein; domain 3 / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
4-(2,4-DICHLOROPHENOXY)-2'-METHYLBIPHENYL-3-OL / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / : / Enoyl-acyl carrier reductase
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsFreundlich, J.S. / Shieh, H. / Anderson, J.W. / Kuo, M. / Yu, M. / Valderramos, J. / Karagyozov, L. / Tsai, H. / Lucumi, E. / Jacobs Jr., W.R. ...Freundlich, J.S. / Shieh, H. / Anderson, J.W. / Kuo, M. / Yu, M. / Valderramos, J. / Karagyozov, L. / Tsai, H. / Lucumi, E. / Jacobs Jr., W.R. / Schiehser, G.A. / Jacobus, D.P. / Fidock, D.A. / Sacchettini, J.C.
CitationJournal: J.Biol.Chem. / Year: 2007
Title: X-ray Structural Analysis of Plasmodium falciparum Enoyl Acyl Carrier Protein Reductase as a Pathway toward the Optimization of Triclosan Antimalarial Efficacy.
Authors: Freundlich, J.S. / Wang, F. / Tsai, H.C. / Kuo, M. / Shieh, H.M. / Anderson, J.W. / Nkrumah, L.J. / Valderramos, J.C. / Yu, M. / Kumar, T.R. / Valderramos, S.G. / Jacobs, W.R. / Schiehser, G. ...Authors: Freundlich, J.S. / Wang, F. / Tsai, H.C. / Kuo, M. / Shieh, H.M. / Anderson, J.W. / Nkrumah, L.J. / Valderramos, J.C. / Yu, M. / Kumar, T.R. / Valderramos, S.G. / Jacobs, W.R. / Schiehser, G.A. / Jacobus, D.P. / Fidock, D.A. / Sacchettini, J.C.
History
DepositionJan 13, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 16, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Revision 1.4Aug 30, 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_ncs_dom_lim / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _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

Downloads & links

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Assembly

Deposited unit
A: enoyl-acyl carrier reductase
B: enoyl-acyl carrier reductase
C: enoyl-acyl carrier reductase
D: enoyl-acyl carrier reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,4058
Polymers74,3884
Non-polymers2,0174
Water99155
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13530 Å2
ΔGint-83 kcal/mol
Surface area24280 Å2
MethodPISA
2
A: enoyl-acyl carrier reductase
B: enoyl-acyl carrier reductase
C: enoyl-acyl carrier reductase
D: enoyl-acyl carrier reductase
hetero molecules

A: enoyl-acyl carrier reductase
B: enoyl-acyl carrier reductase
C: enoyl-acyl carrier reductase
D: enoyl-acyl carrier reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)152,81116
Polymers148,7768
Non-polymers4,0358
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_665-y+1,-x+1,-z+1/21
Buried area37590 Å2
ΔGint-245 kcal/mol
Surface area38020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)130.861, 130.861, 82.687
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12C
22D
33
44

NCS domain segments:

Component-ID: 1 / Refine code: 4

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLUGLULYSLYSAA97 - 3251 - 229
21GLUGLULYSLYSBB97 - 3251 - 229
12TYRTYRASPASPCC366 - 4251 - 60
22TYRTYRASPASPDD366 - 4251 - 60

NCS ensembles :
ID
1
2
3
4
DetailsThe biological assembly is a tetramer generated from the dimer in the asymmetric subunit

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Components

#1: Protein enoyl-acyl carrier reductase


Mass: 30364.375 Da / Num. of mol.: 2 / Fragment: N-terminal fragment, residues 97-216
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum)
Strain: 3D7 / Gene: PfENR / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) Codon+-RIL cells
References: GenBank: 23612231, UniProt: C6KSZ2*PLUS, enoyl-[acyl-carrier-protein] reductase (NADH)
#2: Protein enoyl-acyl carrier reductase


Mass: 6829.676 Da / Num. of mol.: 2 / Fragment: C-terminal fragment, residues 97-156
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum)
Strain: 3D7 / Gene: PfENR / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) Codon+-RIL cells
References: GenBank: 23612231, UniProt: C6KSZ2*PLUS, enoyl-[acyl-carrier-protein] reductase (NADH)
#3: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#4: Chemical ChemComp-JPA / 4-(2,4-DICHLOROPHENOXY)-2'-METHYLBIPHENYL-3-OL


Mass: 345.219 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C19H14Cl2O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 55 / 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: 2.4 Å3/Da / Density % sol: 48.65 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 2.35 M (NH4)2SO4, 100 sodium acetate buffer, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Oct 10, 2004
RadiationMonochromator: Osmic mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.5→33.8 Å / Num. all: 25282 / Num. obs: 23997

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1NHD

1nhd
PDB Unreleased entry


Resolution: 2.5→33.77 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.907 / SU B: 8.486 / SU ML: 0.195 / Cross valid method: THROUGHOUT / ESU R: 0.485 / ESU R Free: 0.289 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25493 1285 5.1 %RANDOM
Rwork0.19343 ---
all0.19655 ---
obs0.19655 23997 99.28 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 37.069 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.5→33.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4576 0 134 55 4765
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0224808
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5171.9996506
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.675574
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.24924.808208
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.42715852
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.7011520
X-RAY DIFFRACTIONr_chiral_restr0.1020.2714
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023568
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.260.32417
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3360.53379
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2020.5333
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2710.3148
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2430.525
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.81952927
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it4.24974624
X-RAY DIFFRACTIONr_scbond_it5.88892155
X-RAY DIFFRACTIONr_scangle_it7.718111882
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A1807medium positional0.350.5
21C482medium positional0.240.5
33A44medium positional0.140.5
44A23medium positional0.070.5
11A1807medium thermal1.182
21C482medium thermal1.042
33A44medium thermal1.412
44A23medium thermal0.872
LS refinement shellResolution: 2.5→2.56 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.316 83 -
Rwork0.234 1711 -
obs--97.87 %

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