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- PDB-1zxb: Synthesis, Biological Activity, and X-Ray Crystal Structural Anal... -

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Basic information

Entry
Database: PDB / ID: 1zxb
TitleSynthesis, Biological Activity, and X-Ray Crystal Structural Analysis of Diaryl Ether Inhibitors of Malarial Enoyl ACP Reductase. Part 1:4'-Substituted Triclosan Derivatives
Componentsenoyl-acyl carrier reductase
KeywordsOXIDOREDUCTASE
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 / Chem-TN3 / : / Enoyl-ACP reductase
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.68 Å
AuthorsFreundlich, J.S. / Anderson, J.W. / Sarantakis, D. / Shieh, H.M. / Yu, M. / Lucumi, E. / Kuo, M. / Schiehser, G.A. / Jacobus, D.P. / Jacobs Jr., W.R. ...Freundlich, J.S. / Anderson, J.W. / Sarantakis, D. / Shieh, H.M. / Yu, M. / Lucumi, E. / Kuo, M. / Schiehser, G.A. / Jacobus, D.P. / Jacobs Jr., W.R. / Fidock, D.A. / Sacchettini, J.C.
CitationJournal: Bioorg.Med.Chem.Lett. / Year: 2005
Title: Synthesis, biological activity, and X-ray crystal structural analysis of diaryl ether inhibitors of malarial enoyl acyl carrier protein reductase. Part 1: 4'-Substituted triclosan derivatives.
Authors: Freundlich, J.S. / Anderson, J.W. / Sarantakis, D. / Shieh, H.M. / Yu, M. / Valderramos, J.C. / Lucumi, E. / Kuo, M. / Jacobs, W.R. / Fidock, D.A. / Schiehser, G.A. / Jacobus, D.P. / Sacchettini, J.C.
History
DepositionJun 7, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 13, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Revision 1.4Aug 23, 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_ncs_dom_lim / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,1436
Polymers76,1922
Non-polymers1,9514
Water00
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)156,28612
Polymers152,3844
Non-polymers3,9028
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_665-y+1,-x+1,-z+1/21
Buried area24480 Å2
ΔGint-184 kcal/mol
Surface area38670 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)131.427, 131.427, 82.948
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
12B
13A
14B

NCS domain segments:

Dom-ID: 1 / Component-ID: 1 / Refine code: 4

Ens-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1GLUGLULYSLYSAA97 - 3251 - 229
2GLUGLULYSLYSBB97 - 3251 - 229
3TYRTYRASPASPAA366 - 425270 - 329
4TYRTYRASPASPBB366 - 425270 - 329

NCS ensembles :
ID
1
2
3
4

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Components

#1: Protein enoyl-acyl carrier reductase


Mass: 38095.957 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum)
Gene: PfENR / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) Codon+-RIL cells
References: GenBank: 23612231, UniProt: Q9BH77*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-TN3 / 3-CHLORO-4-(4-CHLORO-2-HYDROXYPHENOXY)-N-METHYLBENZAMIDE


Mass: 312.148 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H11Cl2NO3

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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: 2.7 Å3/Da / Density % sol: 54 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 5.6 / Details: pH 5.60, VAPOR DIFFUSION, HANGING DROP

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Mar 29, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.68→92.848 Å / Num. obs: 20933

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Processing

Software
NameVersionClassification
AMoREphasing
REFMAC5.2.0005refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1NHD

1nhd
PDB Unreleased entry


Resolution: 2.68→30 Å / Cor.coef. Fo:Fc: 0.888 / Cor.coef. Fo:Fc free: 0.833 / SU B: 14.645 / SU ML: 0.31 / Cross valid method: THROUGHOUT / ESU R: 1.384 / ESU R Free: 0.4 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.301 1068 5.1 %RANDOM
Rwork0.233 ---
obs0.236 19816 99.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 32.97 Å2
Baniso -1Baniso -2Baniso -3
1-0.34 Å20 Å20 Å2
2--0.34 Å20 Å2
3----0.69 Å2
Refinement stepCycle: LAST / Resolution: 2.68→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4574 0 128 0 4702
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0224800
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4451.9976494
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2365574
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.59624.808208
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.86115852
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.4321520
X-RAY DIFFRACTIONr_chiral_restr0.0950.2714
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.023558
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2290.22364
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3170.23304
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1580.2188
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2190.2148
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2480.216
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.40852932
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.74474624
X-RAY DIFFRACTIONr_scbond_it4.59692182
X-RAY DIFFRACTIONr_scangle_it6.194111870
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDType
11A1807X-RAY DIFFRACTIONmedium positional
21A482X-RAY DIFFRACTIONmedium positional
31A44X-RAY DIFFRACTIONmedium positional
41A20X-RAY DIFFRACTIONmedium positional
11A1807X-RAY DIFFRACTIONmedium thermal
21A482X-RAY DIFFRACTIONmedium thermal
31A44X-RAY DIFFRACTIONmedium thermal
41A20X-RAY DIFFRACTIONmedium thermal
LS refinement shellResolution: 2.68→2.75 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.312 69 -
Rwork0.221 1411 -
obs--99.8 %

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