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- PDB-3am5: K316A mutant of Enoyl-ACP Reductase from Plasmodium falciparum (P... -

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Basic information

Entry
Database: PDB / ID: 3am5
TitleK316A mutant of Enoyl-ACP Reductase from Plasmodium falciparum (PfENR) in complex with triclosan
ComponentsEnoyl-ACP reductase
KeywordsOXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR / Triclosan / Enoyl-ACP reductase / mutant / oxidoreductase / P.falciparum / FabI / OXIDOREDUCTASE-OXIDOREDUCTASE INHIBITOR complex
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
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / TRICLOSAN / Enoyl-ACP reductase
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsMaity, K. / Banerjee, T. / Narayanappa, P. / Surolia, N. / Surolia, A. / Suguna, K.
CitationJournal: Iubmb Life / Year: 2011
Title: Effect of substrate binding loop mutations on the structure, kinetics, and inhibition of enoyl acyl carrier protein reductase from plasmodium falciparum
Authors: Maity, K. / Banerjee, T. / Prabakaran, N. / Surolia, N. / Surolia, A. / Suguna, K.
History
DepositionAug 14, 2010Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 16, 2011Provider: 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_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

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)76,2786
Polymers74,3722
Non-polymers1,9064
Water8,125451
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)152,55612
Polymers148,7444
Non-polymers3,8128
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_665-y+1,-x+1,-z+1/21
Buried area16140 Å2
ΔGint-97 kcal/mol
Surface area39850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)131.110, 131.110, 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 / PfENR


Mass: 37186.086 Da / Num. of mol.: 2 / Fragment: residues 96-424 / Mutation: K316A
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-TCL / TRICLOSAN


Mass: 289.542 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H7Cl3O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 451 / 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: 48.57 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 5.8
Details: 3M ammonium sulphate, 0.1M MES buffer, 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 18, 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: 2.05→51.4 Å / Num. obs: 45800 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 9.8 % / Biso Wilson estimate: 26.6 Å2 / Rmerge(I) obs: 0.083 / Net I/σ(I): 20.3
Reflection shellResolution: 2.05→2.16 Å / Redundancy: 9.7 % / Rmerge(I) obs: 0.461 / Mean I/σ(I) obs: 4.4 / Num. unique all: 6576 / % 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: 2.05→47.85 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.943 / SU B: 3.554 / SU ML: 0.097 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.148 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.20693 2300 5 %RANDOM
Rwork0.16414 ---
obs0.16626 43270 99.48 %-
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: 30.804 Å2
Baniso -1Baniso -2Baniso -3
1-0.89 Å20 Å20 Å2
2--0.89 Å20 Å2
3----1.78 Å2
Refinement stepCycle: LAST / Resolution: 2.05→47.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4442 0 122 451 5015
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0224711
X-RAY DIFFRACTIONr_angle_refined_deg1.5441.9936395
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8035584
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.24124.518197
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.47715803
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.6581521
X-RAY DIFFRACTIONr_chiral_restr0.1040.2714
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0213503
X-RAY DIFFRACTIONr_mcbond_it0.9271.52866
X-RAY DIFFRACTIONr_mcangle_it1.71324602
X-RAY DIFFRACTIONr_scbond_it2.39631845
X-RAY DIFFRACTIONr_scangle_it3.7854.51787
LS refinement shellResolution: 2.05→2.103 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.27 183 -
Rwork0.207 3102 -
obs--99.3 %

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