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- PDB-1zw1: Synthesis, Biological Activity, and X-Ray Crystal Structural Anal... -

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Basic information

Entry
Database: PDB / ID: 1zw1
TitleSynthesis, Biological Activity, and X-Ray Crystal Structural Analysis of Diaryl Ether Inhibitors of Malarial Enoyl ACP Reductase. Part 1:4'-Substituted Triclosan Derivatives
Componentsenoyl-acyl carrier reductase
KeywordsOXIDOREDUCTASE
Function / homology
Function and homology information


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 / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / 2-(4-AMINO-2-CHLOROPHENOXY)-5-CHLOROPHENOL / Enoyl-ACP reductase
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsFreundlich, J.S. / Anderson, J.W. / Sarantakis, D. / Shieh, H.M. / Yu, M. / Lucumi, E. / Kuo, M. / Schiehser, G.A. / Jacobus, D.P. / Jacobs Jr., W.R. ...Freundlich, J.S. / Anderson, J.W. / Sarantakis, D. / Shieh, H.M. / Yu, M. / Lucumi, E. / Kuo, M. / Schiehser, G.A. / Jacobus, D.P. / Jacobs Jr., W.R. / Fidock, D.A. / Sacchettini, J.C.
CitationJournal: Bioorg.Med.Chem.Lett. / Year: 2005
Title: Synthesis, biological activity, and X-ray crystal structural analysis of diaryl ether inhibitors of malarial enoyl acyl carrier protein reductase. Part 1: 4'-Substituted triclosan derivatives.
Authors: Freundlich, J.S. / Anderson, J.W. / Sarantakis, D. / Shieh, H.M. / Yu, M. / Valderramos, J.C. / Lucumi, E. / Kuo, M. / Jacobs, W.R. / Fidock, D.A. / Schiehser, G.A. / Jacobus, D.P. / Sacchettini, J.C.
History
DepositionJun 3, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 6, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Aug 23, 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,0596
Polymers76,1922
Non-polymers1,8674
Water00
1
A: enoyl-acyl carrier reductase
B: enoyl-acyl carrier reductase
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)156,11812
Polymers152,3844
Non-polymers3,7348
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_665-y+1,-x+1,-z+1/21
Buried area24240 Å2
ΔGint-171 kcal/mol
Surface area39070 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)131.266, 131.266, 82.897
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein enoyl-acyl carrier reductase


Mass: 38095.957 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum)
Gene: PfENR / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) Codon+-RIL cells
References: UniProt: Q9BH77, enoyl-[acyl-carrier-protein] reductase (NADH)
#2: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Chemical ChemComp-TN5 / 2-(4-AMINO-2-CHLOROPHENOXY)-5-CHLOROPHENOL


Mass: 270.111 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H9Cl2NO2

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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: 2.7 Å3/Da / Density % sol: 53 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: pH 5.60, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: MACSCIENCE / Detector: IMAGE PLATE / Date: Mar 29, 2005 / Details: OSMIC
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.899→29.722 Å / Num. obs: 16254

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Processing

Software
NameClassification
XDIPdata collection
SCALEPACKdata scaling
CNSrefinement
XDIPdata reduction
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1nhd

1nhd
PDB Unreleased entry


Resolution: 2.9→29.722 Å / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.297 1524 9.2 %RANDOM
Rwork0.228 ---
obs0.228 15320 92.5 %-
Solvent computationBsol: 15.67 Å2
Displacement parametersBiso mean: 30 Å2
Baniso -1Baniso -2Baniso -3
1-0.139 Å20 Å20 Å2
2--0.139 Å20 Å2
3----0.278 Å2
Refinement stepCycle: LAST / Resolution: 2.9→29.722 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4574 0 122 0 4696
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1CNS_TOPPAR:PROTEIN_REP.PARAM
X-RAY DIFFRACTION2NAD.PAR
X-RAY DIFFRACTION3TNA.PAR

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