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- PDB-1nnu: Crystal Structure Analysis of Plasmodium falciparum enoyl-acyl-ca... -

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Basic information

Entry
Database: PDB / ID: 1nnu
TitleCrystal Structure Analysis of Plasmodium falciparum enoyl-acyl-carrier-protein reductase with Triclosan Analog
Components(enoyl-acyl carrier reductase) x 2
KeywordsOXIDOREDUCTASE / rossmann fold / nadh / short chain dehydrogenase reductase
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 / Enoyl-[acyl-carrier-protein] reductase (NADH) / Enoyl-(Acyl carrier protein) reductase / Helicase, Ruva Protein; domain 3 / Short-chain dehydrogenase/reductase SDR / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich ...Enoyl acyl carrier protein reductase / Enoyl-[acyl-carrier-protein] reductase (NADH) / Enoyl-(Acyl carrier protein) reductase / Helicase, Ruva Protein; domain 3 / Short-chain dehydrogenase/reductase SDR / 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
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / 6-(4-CHLORO-2-HYDROXY-PHENOXY)-NAPHTHALEN-2-OL / Enoyl-ACP reductase
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsPerozzo, R. / Kuo, M. / Sidhu, A.S. / Valiyaveettil, J.T. / Bittman, R. / Jacobs Jr., W.R. / Fidock, D.A. / Sacchettini, J.C.
CitationJournal: J.Biol.Chem. / Year: 2002
Title: Structural Elucidation of the Specificity of the Antibacterial Agent Triclosan for Malarial Enoyl Acyl Carrier Protein Reductase
Authors: Perozzo, R. / Kuo, M. / Sidhu, A.S. / Valiyaveettil, J.T. / Bittman, R. / Jacobs Jr., W.R. / Fidock, D.A. / Sacchettini, J.C.
History
DepositionJan 14, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 25, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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
C: enoyl-acyl carrier reductase
D: enoyl-acyl carrier reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,0498
Polymers65,1484
Non-polymers1,9004
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13380 Å2
ΔGint-73 kcal/mol
Surface area24940 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)134,09816
Polymers130,2978
Non-polymers3,8018
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_665-y+1,-x+1,-z+1/21
Buried area37190 Å2
ΔGint-222 kcal/mol
Surface area39440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)133.097, 133.097, 83.689
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 / enoyl-ACP-reductase


Mass: 25744.570 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum)
Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) Codon+-RIL
References: UniProt: Q9BH77, enoyl-[acyl-carrier-protein] reductase (NADH)
#2: Protein enoyl-acyl carrier reductase / enoyl-ACP-reductase


Mass: 6829.676 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum)
Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) Codon+-RIL
References: UniProt: Q9BH77, 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-TCT / 6-(4-CHLORO-2-HYDROXY-PHENOXY)-NAPHTHALEN-2-OL


Mass: 286.710 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H11ClO3

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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: 2.84 Å3/Da / Density % sol: 56.75 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 100 mM sodium acetate, 2.35 M ammonium sulfate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
pH: 7.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
120 mMTris-HCl1droppH7.5
2150 mM1dropNaCl
320 mg/mlprotein1drop
44 mMNAD+1drop
51 mMtriclosan1drop
62.35 Mammonium sulfate1reservoir
7100 mMMES1reservoirpH5.6

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: ROTATING ANODE / Type: MACSCIENCE / Wavelength: 1.54 Å
DetectorType: MACSCIENCE / Detector: IMAGE PLATE / Date: Mar 6, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.5→30 Å / Num. all: 26564 / Num. obs: 25188 / % possible obs: 94.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection
*PLUS
Num. obs: 26564 / Redundancy: 3.7 % / Rmerge(I) obs: 0.098

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→30 Å / σ(F): 0
RfactorNum. reflectionSelection details
Rfree0.227 2490 Random
Rwork0.176 --
all-25188 -
obs-25188 -
Refinement stepCycle: LAST / Resolution: 2.5→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4574 0 128 0 4702
Refinement
*PLUS
Lowest resolution: 30 Å / % reflection Rfree: 10 %
Solvent computation
*PLUS
Displacement parameters
*PLUS

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