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- PDB-6t6n: Crystal structure of Klebsiella pneumoniae FabG2(NADH-dependent) ... -

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Basic information

Entry
Database: PDB / ID: 6t6n
TitleCrystal structure of Klebsiella pneumoniae FabG2(NADH-dependent) in complex with NADH at 2.5 A resolution
Components3-oxoacyl-[acyl-carrier protein] reductase
KeywordsBIOSYNTHETIC PROTEIN / Fatty acid biosynthesis / FabG / (3-oxoacyl-(Acyl-carrier-protein) reductase) / NADH / NADPH / complex / FAS-II
Function / homology
Function and homology information


monocarboxylic acid metabolic process / 3-oxoacyl-[acyl-carrier-protein] reductase (NADPH) activity / lipid metabolic process / nucleotide binding
Similarity search - Function
: / : / 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
D-MALATE / 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / 3-oxoacyl-[acyl-carrier-protein] reductase FabG
Similarity search - Component
Biological speciesKlebsiella pneumoniae 30684/NJST258_2 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsVella, P. / Schnell, R. / Lindqvist, Y. / 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 18, 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
B: 3-oxoacyl-[acyl-carrier protein] reductase
C: 3-oxoacyl-[acyl-carrier protein] reductase
D: 3-oxoacyl-[acyl-carrier protein] reductase
E: 3-oxoacyl-[acyl-carrier protein] reductase
F: 3-oxoacyl-[acyl-carrier protein] reductase
G: 3-oxoacyl-[acyl-carrier protein] reductase
H: 3-oxoacyl-[acyl-carrier protein] reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)212,35436
Polymers205,1478
Non-polymers7,20728
Water5,224290
1
A: 3-oxoacyl-[acyl-carrier protein] reductase
B: 3-oxoacyl-[acyl-carrier protein] reductase
C: 3-oxoacyl-[acyl-carrier protein] reductase
D: 3-oxoacyl-[acyl-carrier protein] reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,06417
Polymers102,5734
Non-polymers3,49113
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19620 Å2
ΔGint-98 kcal/mol
Surface area30590 Å2
MethodPISA
2
E: 3-oxoacyl-[acyl-carrier protein] reductase
F: 3-oxoacyl-[acyl-carrier protein] reductase
hetero molecules

E: 3-oxoacyl-[acyl-carrier protein] reductase
F: 3-oxoacyl-[acyl-carrier protein] reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)105,97216
Polymers102,5734
Non-polymers3,39912
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_455-x-1,y,-z1
Buried area18920 Å2
ΔGint-101 kcal/mol
Surface area30720 Å2
MethodPISA
3
G: 3-oxoacyl-[acyl-carrier protein] reductase
H: 3-oxoacyl-[acyl-carrier protein] reductase
hetero molecules

G: 3-oxoacyl-[acyl-carrier protein] reductase
H: 3-oxoacyl-[acyl-carrier protein] reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,60822
Polymers102,5734
Non-polymers4,03518
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z1
Buried area20840 Å2
ΔGint-103 kcal/mol
Surface area30910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)161.109, 255.316, 262.312
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number22
Space group name H-MF222

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Components

#1: Protein
3-oxoacyl-[acyl-carrier protein] reductase


Mass: 25643.330 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Details: FabG2 from Klebsiella pneumoniae is a homologue of the fatty acid bisynthesis enzyme FabG, however NADH-dependent. It catalyses the reduction of 3-oxo-acyl(C4)-CoA substrate.
Source: (gene. exp.) Klebsiella pneumoniae 30684/NJST258_2 (bacteria)
Gene: KPNJ2_02761 / Plasmid: pNIC28-Bsa4
Details (production host): N-terminal His6-tag, removable by TEV cleavage
Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: W8VGR4, 3-oxoacyl-[acyl-carrier-protein] reductase
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 19 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical
ChemComp-NAI / 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / NADH


Mass: 665.441 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C21H29N7O14P2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-MLT / D-MALATE / (2R)-2-HYDROXYBUTANEDIOIC ACID / 2-HYDROXY-SUCCINIC ACID


Mass: 134.087 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O5
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 290 / 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: 3.24 Å3/Da / Density % sol: 0.63 % / Description: short rods
Crystal growTemperature: 297 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 20 % PEG3350 0.2 M Na malonate pH 6.0 12.5 mM NADH added to the protein solution prior to drop mixing

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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 mirrors
RadiationMonochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 2.5→48.96 Å / Num. obs: 92045 / % possible obs: 99.3 % / Redundancy: 4.3 % / Biso Wilson estimate: 46.1 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.075 / Rpim(I) all: 0.044 / Rrim(I) all: 0.096 / Net I/σ(I): 10.2
Reflection shellResolution: 2.5→2.54 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.606 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 4546 / CC1/2: 0.739 / Rpim(I) all: 0.369 / Rrim(I) all: 0.779 / % possible all: 99.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0155refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4JRO

4jro


Resolution: 2.5→30 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.956 / SU B: 8.554 / SU ML: 0.179 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.368 / ESU R Free: 0.224
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2106 4508 4.9 %RANDOM
Rwork0.1917 ---
obs0.1927 87489 99.13 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 135.51 Å2 / Biso mean: 55.47 Å2 / Biso min: 13.29 Å2
Baniso -1Baniso -2Baniso -3
1--0.15 Å2-0 Å20 Å2
2--0.74 Å2-0 Å2
3----0.59 Å2
Refinement stepCycle: final / Resolution: 2.5→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14288 0 475 290 15053
Biso mean--54.02 41.77 -
Num. residues----1952
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.01915080
X-RAY DIFFRACTIONr_bond_other_d0.0020.0214661
X-RAY DIFFRACTIONr_angle_refined_deg1.4781.98120433
X-RAY DIFFRACTIONr_angle_other_deg0.938333535
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.48551980
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.66724.245596
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.841152466
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.60515111
X-RAY DIFFRACTIONr_chiral_restr0.0740.22377
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0217291
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023392
LS refinement shellResolution: 2.5→2.564 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.335 322 -
Rwork0.319 6435 -
all-6757 -
obs--99.34 %

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