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

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Basic information

Entry
Database: PDB / ID: 2oos
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 / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
2-(2,4-DICHLOROPHENOXY)-5-(2-PHENYLETHYL)PHENOL / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Enoyl-ACP reductase / Enoyl-ACP reductase
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 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)78,7446
Polymers76,6992
Non-polymers2,0454
Water3,189177
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)157,48812
Polymers153,3974
Non-polymers4,0918
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_665-y+1,-x+1,-z+1/21
Buried area25190 Å2
ΔGint-194 kcal/mol
Surface area37720 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)131.221, 131.221, 83.163
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, UniProt: Q9BJJ9*PLUS, 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-JPJ / 2-(2,4-DICHLOROPHENOXY)-5-(2-PHENYLETHYL)PHENOL


Mass: 359.246 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H16Cl2O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 177 / 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: 2.33 Å3/Da / Density % sol: 47.28 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 2.35M (NH4)2SO4, 0.1M AcONa, pH 5.6, 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
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. all: 43027 / Num. obs: 42970 / % possible obs: 99.87 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 7.2 % / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
CrystalCleardata collection
HKL-2000data reduction
HKL-2000data scaling
XFITdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1NHD

1nhd
PDB Unreleased entry


Resolution: 2.1→92.85 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.939 / SU B: 3.816 / SU ML: 0.105 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.194 / ESU R Free: 0.167 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22747 2160 5 %RANDOM
Rwork0.19229 ---
all0.998 42846 --
obs0.19402 40686 99.73 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 39.937 Å2
Baniso -1Baniso -2Baniso -3
1-0.57 Å20 Å20 Å2
2--0.57 Å20 Å2
3----1.14 Å2
Refinement stepCycle: LAST / Resolution: 2.1→92.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4492 0 136 177 4805
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0224721
X-RAY DIFFRACTIONr_angle_refined_deg1.8041.9986386
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2835564
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.38524.778203
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.0115831
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.9591520
X-RAY DIFFRACTIONr_chiral_restr0.1590.2705
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023492
X-RAY DIFFRACTIONr_nbd_refined0.2110.22236
X-RAY DIFFRACTIONr_nbtor_refined0.310.23244
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1530.2235
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2760.2159
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2590.245
X-RAY DIFFRACTIONr_mcbond_it1.1811.52930
X-RAY DIFFRACTIONr_mcangle_it1.924545
X-RAY DIFFRACTIONr_scbond_it2.84432135
X-RAY DIFFRACTIONr_scangle_it4.0424.51841
LS refinement shellResolution: 2.099→2.153 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.287 164 -
Rwork0.21 2960 -
obs--99.97 %

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