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- PDB-3lt4: Enoyl-ACP Reductase from Plasmodium falciparum (PfENR) in complex... -

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Basic information

Entry
Database: PDB / ID: 3lt4
TitleEnoyl-ACP Reductase from Plasmodium falciparum (PfENR) in complex with triclosan variant PB4
ComponentsEnoyl-ACP reductase
KeywordsOXIDOREDUCTASE / Triclosan / Triclosan variant / Enoyl-ACP reductase / P.falciparum
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-amino-4-chlorophenoxy)-5-chlorophenol / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Enoyl-ACP reductase
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsMaity, K. / Bhargav, S.P. / Surolia, N. / Surolia, A. / Suguna, K.
CitationJournal: Iubmb Life / Year: 2010
Title: X-ray crystallographic analysis of the complexes of enoyl acyl carrier protein reductase of Plasmodium falciparum with triclosan variants to elucidate the importance of different functional ...Title: X-ray crystallographic analysis of the complexes of enoyl acyl carrier protein reductase of Plasmodium falciparum with triclosan variants to elucidate the importance of different functional groups in enzyme inhibition
Authors: Maity, K. / Bhargav, S.P. / Sankaran, B. / Surolia, N. / Surolia, A. / Suguna, K.
History
DepositionFeb 15, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 16, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 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-ACP reductase
B: Enoyl-ACP reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,3556
Polymers74,4882
Non-polymers1,8674
Water7,999444
1
A: Enoyl-ACP reductase
B: Enoyl-ACP reductase
hetero molecules

A: Enoyl-ACP reductase
B: Enoyl-ACP reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)152,71112
Polymers148,9774
Non-polymers3,7348
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_665-y+1,-x+1,-z+1/21
Buried area16590 Å2
ΔGint-96 kcal/mol
Surface area40250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)131.180, 131.180, 82.780
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-ACP reductase


Mass: 37244.184 Da / Num. of mol.: 2 / Fragment: residues 96-424
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum)
Gene: fabI / Plasmid: PET-28a(+)(NOVAGEN) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q9BJJ9, 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-FB4 / 2-(2-amino-4-chlorophenoxy)-5-chlorophenol


Mass: 270.111 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H9Cl2NO2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 444 / 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: 2.39 Å3/Da / Density % sol: 48.55 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 5.8
Details: 2.9M ammonium sulphate, 0.1M sodium acetate, pH 5.8, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.54 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Mar 17, 2009 / Details: Mirror
RadiationMonochromator: OSMIC MIRROR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.25→58.6 Å / Num. obs: 34875 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 13.2 % / Biso Wilson estimate: 28.7 Å2 / Rmerge(I) obs: 0.059 / Net I/σ(I): 33.2
Reflection shellResolution: 2.25→2.37 Å / Redundancy: 12.6 % / Rmerge(I) obs: 0.205 / Mean I/σ(I) obs: 14.1 / Num. unique all: 5012 / % possible all: 100

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
PHASERphasing
REFMAC5.5.0044refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1UH5

1uh5


Resolution: 2.25→51.41 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.933 / SU B: 4.423 / SU ML: 0.113 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.223 / ESU R Free: 0.186 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.20664 1752 5 %RANDOM
Rwork0.15315 ---
obs0.15582 33117 99.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 28.357 Å2
Baniso -1Baniso -2Baniso -3
1-0.85 Å20 Å20 Å2
2--0.85 Å20 Å2
3----1.71 Å2
Refinement stepCycle: LAST / Resolution: 2.25→51.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4458 0 122 444 5024
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0224780
X-RAY DIFFRACTIONr_angle_refined_deg1.461.9916501
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3835601
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.10424.433203
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.34115820
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.4571523
X-RAY DIFFRACTIONr_chiral_restr0.0990.2726
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0213571
X-RAY DIFFRACTIONr_mcbond_it0.8281.52899
X-RAY DIFFRACTIONr_mcangle_it1.55124667
X-RAY DIFFRACTIONr_scbond_it2.22931881
X-RAY DIFFRACTIONr_scangle_it3.5444.51821
LS refinement shellResolution: 2.25→2.308 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.211 140 -
Rwork0.149 2399 -
obs--99.96 %

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