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

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Basic information

Entry
Database: PDB / ID: 4igf
TitleCrystal structure of Plasmodium falciparum FabI complexed with NAD and inhibitor 3-(4-Chloro-2-hydroxyphenoxy)-7-hydroxy-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 [NAD(P)H] activity / 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 / 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
Chem-CHV / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Enoyl-acyl carrier reductase
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 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

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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)80,94311
Polymers78,5392
Non-polymers2,4059
Water4,378243
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6440 Å2
ΔGint-45 kcal/mol
Surface area24760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)131.556, 131.556, 82.635
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, 252 molecules

#2: Chemical ChemComp-CHV / 3-(4-chloro-2-hydroxyphenoxy)-7-hydroxy-2H-chromen-2-one


Mass: 304.682 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H9ClO5
#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.: 3 / 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.: 243 / 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: 45.96 %
Crystal growTemperature: 291 K / Method: vapor diffusion / pH: 5.6
Details: 0.1M MES, 2.35M ammonium sulfate, pH 5.6, VAPOR DIFFUSION, 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: 2.3→70 Å / Num. all: 32749 / Num. obs: 32749 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 14.73 % / Biso Wilson estimate: 41 Å2 / Rsym value: 0.135 / Net I/σ(I): 22.48
Reflection shellResolution: 2.3→2.36 Å / Redundancy: 14.91 % / Mean I/σ(I) obs: 3.27 / Num. unique all: 2389 / Rsym value: 1.09 / % possible all: 99.9

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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: 2.3→69.976 Å / Occupancy max: 1 / Occupancy min: 0.33 / SU ML: 0.25
Isotropic thermal model: TLS groups for protein chains A and B, individual isotropic temperature factors
Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 19.06 / Stereochemistry target values: Engh & Huber
Details: Mask bulk solvent model. Maximum-likelhood based coordinate error 0.25 A.
RfactorNum. reflection% reflectionSelection details
Rfree0.2024 1661 5.07 %random
Rwork0.1532 ---
all0.1557 32744 --
obs0.1557 32744 99.91 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 152.99 Å2 / Biso mean: 30.9842 Å2 / Biso min: 2.42 Å2
Refinement stepCycle: LAST / Resolution: 2.3→69.976 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4460 0 158 243 4861
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.014751
X-RAY DIFFRACTIONf_angle_d1.3886431
X-RAY DIFFRACTIONf_dihedral_angle_d14.2191814
X-RAY DIFFRACTIONf_chiral_restr0.095704
X-RAY DIFFRACTIONf_plane_restr0.006845
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 12 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.3001-2.36780.2641430.205225412684
2.3678-2.44420.32321280.203525582686
2.4442-2.53160.23911440.191925252669
2.5316-2.63290.25321540.176825532707
2.6329-2.75280.23081560.170425352691
2.7528-2.89790.23171220.167125592681
2.8979-3.07950.25541340.164125692703
3.0795-3.31720.18111320.152526002732
3.3172-3.6510.20291370.138625892726
3.651-4.17930.16991400.118926052745
4.1793-5.26520.14351360.118126542790
5.2652-70.00790.19331350.172827952930
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)
10.4225-0.22850.14910.5422-0.30190.6471-0.0239-0.0539-0.02770.1096-0.0133-0.07810.01030.0865-0.02950.07760.004-0.02720.06930.00620.080244.134984.804637.8659
20.8773-0.44930.03260.6127-0.00690.1943-0.0636-0.1373-0.08910.08790.07220.12920.0204-0.13630.00860.0618-0.00230.00980.1203-0.00980.071114.4456102.750234.7069
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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