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- PDB-2op1: Crystal structure of plasmodium falciparum enoyl ACP reductase wi... -

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Basic information

Entry
Database: PDB / ID: 2op1
TitleCrystal structure of plasmodium falciparum enoyl ACP reductase with triclosan reductase
ComponentsEnoyl-acyl carrier reductase
KeywordsOXIDOREDUCTASE / PfENR / malaria / triclosan analog
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 / Short-chain dehydrogenase/reductase SDR / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-8PC / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Enoyl-ACP reductase
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsTsai, H.
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.S. / Valderramos, S.G. / Jacobs, W.R. / ...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.S. / Valderramos, S.G. / Jacobs, W.R. / Schiehser, G.A. / Jacobus, D.P. / Fidock, D.A. / Sacchettini, J.C.
History
DepositionJan 26, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 17, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Aug 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_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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

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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)78,7186
Polymers76,6992
Non-polymers2,0194
Water2,216123
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)157,43612
Polymers153,3974
Non-polymers4,0398
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_665-y+1,-x+1,-z+1/21
Buried area24440 Å2
ΔGint-192 kcal/mol
Surface area37170 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)131.498, 131.498, 82.334
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: 38349.309 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum)
Gene: FabI / 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-8PC / 2-(2,4-DICHLOROPHENOXY)-5-(PYRIDIN-2-YLMETHYL)PHENOL


Mass: 346.207 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C18H13Cl2NO2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 123 / 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: 2.32 Å3/Da / Density % sol: 46.98 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop
Details: 2.35M (NH4)2SO4, 0.1M AcONa, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54178 Å
DetectorType: RIGAKU / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 2.6→30 Å / Num. all: 22663 / Num. obs: 22516 / % possible obs: 99.4 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1
Reflection shellResolution: 2.6→2.69 Å / Redundancy: 6.8 % / Num. unique all: 2213 / % possible all: 99.7

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Processing

Software
NameClassification
HKL-2000data collection
XFITdata reduction
PHENIXrefinement
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1NHD

1nhd
PDB Unreleased entry


Resolution: 2.6→30 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2701 1148 -RANDOM
Rwork0.2071 ---
all0.2071 22520 --
obs0.2071 21372 94.9 %-
Refinement stepCycle: LAST / Resolution: 2.6→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4399 0 134 123 4656
LS refinement shellResolution: 2.6→30 Å

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