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- PDB-4ige: Crystal structure of Plasmodium falciparum FabI complexed with NA... -

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Basic information

Entry
Database: PDB / ID: 4ige
TitleCrystal structure of Plasmodium falciparum FabI complexed with NAD and inhibitor 7-(4-Chloro-2-hydroxyphenoxy)-4-methyl-2H-chromen-2-one
ComponentsEnoyl-acyl carrier reductase
KeywordsOXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR / Reductase / OXIDOREDUCTASE-OXIDOREDUCTASE INHIBITOR complex
Function / homology
Function and homology information


enoyl-[acyl-carrier-protein] reductase activity (NAD(P)H) / apicoplast / enoyl-[acyl-carrier-protein] reductase (NADH) / 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
Chem-CHJ / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Enoyl-acyl carrier reductase
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsKostrewa, D. / Perozzo, R.
CitationJournal: J.Med.Chem. / Year: 2013
Title: Design, Synthesis, and Biological and Crystallographic Evaluation of Novel Inhibitors of Plasmodium falciparum Enoyl-ACP-reductase (PfFabI)
Authors: Belluti, F. / Perozzo, R. / Lauciello, L. / Colizzi, F. / Kostrewa, D. / Bisi, A. / Gobbi, S. / Rampa, A. / Bolognesi, M.L. / Recanatini, M. / Brun, R. / Scapozza, L. / Cavalli, A.
History
DepositionDec 17, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 6, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Category: software
Revision 1.2Nov 8, 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-acyl carrier reductase
B: Enoyl-acyl carrier reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,03112
Polymers78,5392
Non-polymers2,49310
Water4,972276
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6680 Å2
ΔGint-43 kcal/mol
Surface area24950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)131.487, 131.487, 82.858
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Enoyl-acyl carrier reductase


Mass: 39269.262 Da / Num. of mol.: 2 / Fragment: C-terminal fragment, UNP residues 96-432
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum)
Strain: 3D7 / Gene: PfENR, PFF0730c / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21
References: UniProt: C6KSZ2, enoyl-[acyl-carrier-protein] reductase (NADH)

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Non-polymers , 5 types, 286 molecules

#2: Chemical ChemComp-CHJ / 7-(4-chloro-2-hydroxyphenoxy)-4-methyl-2H-chromen-2-one


Mass: 302.709 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H11ClO4
#3: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 276 / 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: 2.28 Å3/Da / Density % sol: 46.05 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 0.1M MES, 2.35M ammonium sulfate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Details: mirrors
RadiationMonochromator: Bartels monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.15→70 Å / Num. all: 39967 / Num. obs: 39967 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 7.35 % / Biso Wilson estimate: 37.4 Å2 / Rsym value: 0.137 / Net I/σ(I): 9.8
Reflection shellResolution: 2.15→2.21 Å / Redundancy: 7.36 % / Mean I/σ(I) obs: 2.8 / Num. unique all: 2892 / Rsym value: 0.756 / % possible all: 99.8

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.8.1_1168)refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1NHG

1nhg


Resolution: 2.15→65.743 Å / Occupancy max: 1 / Occupancy min: 0.5 / SU ML: 0.22
Isotropic thermal model: TLS groups for protein chains A and B, individual isotropic temperature factors
Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 19.99 / Stereochemistry target values: Engh & Huber
Details: Mask bulk solvent model. Maximum-likelhood based coordinate error 0.22 A.
RfactorNum. reflection% reflectionSelection details
Rfree0.2015 2007 5.02 %random
Rwork0.1619 ---
all0.1639 39964 --
obs0.1639 39964 99.83 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 136.37 Å2 / Biso mean: 35.6513 Å2 / Biso min: 10.47 Å2
Refinement stepCycle: LAST / Resolution: 2.15→65.743 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4508 0 164 276 4948
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.014799
X-RAY DIFFRACTIONf_angle_d1.3156495
X-RAY DIFFRACTIONf_dihedral_angle_d13.8271825
X-RAY DIFFRACTIONf_chiral_restr0.083714
X-RAY DIFFRACTIONf_plane_restr0.005852
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.15-2.20380.27171390.220626622801
2.2038-2.26340.26821280.202226742802
2.2634-2.330.26441310.186326692800
2.33-2.40520.24261760.183726392815
2.4052-2.49120.24481350.188926832818
2.4912-2.59090.23451370.176626912828
2.5909-2.70880.21861320.170626792811
2.7088-2.85160.20691520.166726992851
2.8516-3.03030.22361320.162427122844
3.0303-3.26430.20831490.15426972846
3.2643-3.59270.20081430.14927392882
3.5927-4.11250.1611460.13327312877
4.1125-5.18110.15961510.131727722923
5.1811-65.77420.18781560.182529103066
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.5957-0.29730.12320.7331-0.21290.9521-0.0298-0.0722-0.00450.10550.0245-0.05930.0810.1013-00.1596-0.0051-0.02260.15080.00520.149844.437984.846437.9788
20.8753-0.3659-0.15440.6310.02040.556-0.0672-0.1161-0.06290.05580.03510.09950.0011-0.1595-0.00270.09960.007-0.00110.1753-0.01070.126914.4665102.601434.6225
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain AA97 - 424
2X-RAY DIFFRACTION2chain BB97 - 424

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