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- PDB-6t7m: Crystal structure of Salmonella typhimurium FabG at 2.65 A resolution -

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Basic information

Entry
Database: PDB / ID: 6t7m
TitleCrystal structure of Salmonella typhimurium FabG at 2.65 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 / 3-oxoacyl-[acyl-carrier-protein] reductase (NADPH) activity / 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 / Short-chain dehydrogenase/reductase, conserved site / Short-chain dehydrogenases/reductases family signature. / Short-chain dehydrogenase/reductase SDR / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
3-oxoacyl-[acyl-carrier-protein] reductase FabG
Similarity search - Component
Biological speciesSalmonella typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.65 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 22, 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
C: 3-oxoacyl-[acyl-carrier-protein] reductase FabG
D: 3-oxoacyl-[acyl-carrier-protein] reductase FabG


Theoretical massNumber of molelcules
Total (without water)112,5204
Polymers112,5204
Non-polymers00
Water3,567198
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, The mode of tetramer formation is the same as observed for many FabG enzymes form various bacteria
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13430 Å2
ΔGint-75 kcal/mol
Surface area34240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.241, 107.192, 108.619
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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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: 28130.027 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: N-terminal His6-tag (Sequence: MHHHHHHSSGVDLGTENLYFQS)
Source: (gene. exp.) Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720) (bacteria)
Strain: LT2 / SGSC1412 / ATCC 700720 / Gene: fabG, STM1195 / Plasmid: pNIC28Bsa4
Details (production host): N-terminal His6-tag (Sequence: MHHHHHHSSGVDLGTENLYFQS)
Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P0A2C9, 3-oxoacyl-[acyl-carrier-protein] reductase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 198 / 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: 2.57 Å3/Da / Density % sol: 52.09 %
Crystal growTemperature: 297 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.1 M Bis-Tris propane pH 8.50 2 M Sodium Sulfate 20% w/v PEG3350 2% Glycerol Cryoprotection PEG 400 25% included to the Mother liquor: crystals diped in a drop

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Aug 21, 2014 / Details: Sagittally bended Si111 crystal
RadiationMonochromator: Double crystal (Si, 111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 2.65→48.063 Å / Num. obs: 34344 / % possible obs: 99.9 % / Redundancy: 3.7 % / CC1/2: 0.996 / Rmerge(I) obs: 0.091 / Rpim(I) all: 0.062 / Rrim(I) all: 0.122 / Net I/σ(I): 10.5
Reflection shellResolution: 2.65→2.78 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.677 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 4516 / CC1/2: 0.642 / Rpim(I) all: 0.598 / Rrim(I) all: 0.906 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4AFN

4afn


Resolution: 2.65→48.063 Å / SU ML: 0.35 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 26.85
RfactorNum. reflection% reflection
Rfree0.2546 1728 5.05 %
Rwork0.1942 --
obs0.1972 34222 99.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 119.44 Å2 / Biso mean: 53.9141 Å2 / Biso min: 25.83 Å2
Refinement stepCycle: final / Resolution: 2.65→48.063 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7186 0 0 198 7384
Biso mean---51.53 -
Num. residues----981
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.6501-2.72810.331470.28582684100
2.7281-2.81610.31611450.26182666100
2.8161-2.91680.31471500.25742655100
2.9168-3.03350.33681540.23442654100
3.0335-3.17160.29531320.23132701100
3.1716-3.33870.31071200.22522714100
3.3387-3.54790.26211400.21172697100
3.5479-3.82170.29761440.2275264698
3.8217-4.20610.23331650.16712690100
4.2061-4.81420.19411370.14812731100
4.8142-6.06350.22321610.17462757100

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