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- PDB-6t5x: Crystal structure of Salmonella typhimurium FabG in complex with ... -

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Basic information

Entry
Database: PDB / ID: 6t5x
TitleCrystal structure of Salmonella typhimurium FabG in complex with NADPH at 1.5 A resolution
Components3-oxoacyl-[acyl-carrier-protein] reductase FabG
KeywordsBIOSYNTHETIC PROTEIN / Fatty acid biosynthesis / FabG / (3-oxoacyl-(Acyl-carrier-protein) reductase) / NADP / NADPH / complex / FAS-II
Function / homology
Function and homology information


3-oxoacyl-[acyl-carrier-protein] reductase (NADPH) activity / 3-oxoacyl-[acyl-carrier-protein] reductase / fatty acid elongation / oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor / NAD binding / NADP binding / metal ion binding
Similarity search - Function
3-oxoacyl-(acyl-carrier-protein) reductase / : / PKS_KR / Short-chain dehydrogenase/reductase, conserved site / Short-chain dehydrogenases/reductases family signature. / Enoyl-(Acyl carrier protein) reductase / Short-chain dehydrogenase/reductase SDR / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
Chem-NDP / 3-oxoacyl-[acyl-carrier-protein] reductase FabG
Similarity search - Component
Biological speciesSalmonella typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsVella, P. / Schnell, R. / Schneider, G.
Funding support Sweden, 1items
OrganizationGrant numberCountry
Vinnova Sweden
CitationJournal: Bioorg.Med.Chem. / Year: 2021
Title: A FabG inhibitor targeting an allosteric binding site inhibits several orthologs from Gram-negative ESKAPE pathogens.
Authors: Vella, P. / Rudraraju, R.S. / Lundback, T. / Axelsson, H. / Almqvist, H. / Vallin, M. / Schneider, G. / Schnell, R.
History
DepositionOct 17, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 18, 2020Provider: repository / Type: Initial release
Revision 1.1Jun 2, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 3-oxoacyl-[acyl-carrier-protein] reductase FabG
B: 3-oxoacyl-[acyl-carrier-protein] reductase FabG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,9338
Polymers51,1432
Non-polymers1,7906
Water8,215456
1
A: 3-oxoacyl-[acyl-carrier-protein] reductase FabG
B: 3-oxoacyl-[acyl-carrier-protein] reductase FabG
hetero molecules

A: 3-oxoacyl-[acyl-carrier-protein] reductase FabG
B: 3-oxoacyl-[acyl-carrier-protein] reductase FabG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)105,86516
Polymers102,2854
Non-polymers3,58012
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area19060 Å2
ΔGint-69 kcal/mol
Surface area32490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.430, 71.144, 81.366
Angle α, β, γ (deg.)90.000, 94.420, 90.000
Int Tables number5
Space group name H-MI121

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Components

#1: Protein 3-oxoacyl-[acyl-carrier-protein] reductase FabG / 3-ketoacyl-acyl carrier protein reductase / Beta-Ketoacyl-acyl carrier protein reductase / Beta- ...3-ketoacyl-acyl carrier protein reductase / Beta-Ketoacyl-acyl carrier protein reductase / Beta-ketoacyl-ACP reductase


Mass: 25571.277 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720) (bacteria)
Strain: LT2 / SGSC1412 / ATCC 700720 / Gene: fabG, STM1195 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P0A2C9, 3-oxoacyl-[acyl-carrier-protein] reductase
#2: Chemical ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE


Mass: 745.421 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H30N7O17P3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 456 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.18 Å3/Da / Density % sol: 43.69 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2 M LiSO4 0.1 M HEPES pH 7.5 25 %w/v PEG3350 10 mM NADPH (added to the protein solution) Cryoprotection of the crystals: dipping them in 0.2 M LiSO4 0.1 M HEPES pH 7.5 25 %w/v PEG3350 26% Glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.97625 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jul 27, 2016 / Details: toroidal mirror
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 1.5→58.49 Å / Num. obs: 67342 / % possible obs: 95.9 % / Observed criterion σ(I): 2.5 / Redundancy: 2.3 % / CC1/2: 0.999 / Rmerge(I) obs: 0.025 / Rpim(I) all: 0.02 / Rrim(I) all: 0.032 / Net I/σ(I): 18.3
Reflection shellResolution: 1.5→1.53 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.387 / Mean I/σ(I) obs: 2.5 / Num. unique obs: 3464 / CC1/2: 0.843 / Rpim(I) all: 0.335 / Rrim(I) all: 0.491 / % possible all: 97.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4AFN

4afn


Resolution: 1.5→58.21 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.965 / SU B: 1.383 / SU ML: 0.051 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.073 / ESU R Free: 0.073
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.185 3434 5.1 %RANDOM
Rwork0.1588 ---
obs0.1602 63956 95.69 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 80.33 Å2 / Biso mean: 25.223 Å2 / Biso min: 13.71 Å2
Baniso -1Baniso -2Baniso -3
1-0.39 Å20 Å2-0.34 Å2
2--1.15 Å20 Å2
3----1.47 Å2
Refinement stepCycle: final / Resolution: 1.5→58.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3554 0 115 456 4125
Biso mean--31.37 36.44 -
Num. residues----486
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0193748
X-RAY DIFFRACTIONr_bond_other_d0.0020.023594
X-RAY DIFFRACTIONr_angle_refined_deg1.4792.0015072
X-RAY DIFFRACTIONr_angle_other_deg0.93438289
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6125496
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.26324.043141
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.38515646
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.51530
X-RAY DIFFRACTIONr_chiral_restr0.0770.2597
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.024197
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02741
LS refinement shellResolution: 1.5→1.539 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.291 273 -
Rwork0.261 4778 -
all-5051 -
obs--97.64 %

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