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- PDB-8jfi: Crystal structure of 3-oxoacyl-ACP reductase FabG in complex with... -

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Basic information

Entry
Database: PDB / ID: 8jfi
TitleCrystal structure of 3-oxoacyl-ACP reductase FabG in complex with NADP+ and 3-keto-hexanoyl-ACP from Helicobacter pylori
Components
  • 3-oxoacyl-[acyl-carrier-protein] reductase
  • Acyl carrier protein
KeywordsBIOSYNTHETIC PROTEIN / 3-oxoacyl-ACP reductase / FabG / NADP+ / 3-keto-hexanoyl-ACP / Helicobacter pylori
Function / homology
Function and homology information


Kdo2-lipid A biosynthetic process / 3-oxoacyl-[acyl-carrier-protein] reductase / 3-oxoacyl-[acyl-carrier-protein] reductase (NADPH) activity / lipid A biosynthetic process / phosphopantetheine binding / acyl binding / acyl carrier activity / fatty acid biosynthetic process / NAD binding / cytosol
Similarity search - Function
3-oxoacyl-(acyl-carrier-protein) reductase / Polyketide synthase, phosphopantetheine-binding domain / Phosphopantetheine attachment site / PKS_KR / Short-chain dehydrogenase/reductase, conserved site / Short-chain dehydrogenases/reductases family signature. / Acyl carrier protein (ACP) / Enoyl-(Acyl carrier protein) reductase / Phosphopantetheine attachment site / Short-chain dehydrogenase/reductase SDR ...3-oxoacyl-(acyl-carrier-protein) reductase / Polyketide synthase, phosphopantetheine-binding domain / Phosphopantetheine attachment site / PKS_KR / Short-chain dehydrogenase/reductase, conserved site / Short-chain dehydrogenases/reductases family signature. / Acyl carrier protein (ACP) / Enoyl-(Acyl carrier protein) reductase / Phosphopantetheine attachment site / Short-chain dehydrogenase/reductase SDR / Phosphopantetheine attachment site. / Phosphopantetheine attachment site / ACP-like superfamily / Carrier protein (CP) domain profile. / Phosphopantetheine binding ACP domain / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Chem-UHC / 3-oxoacyl-[acyl-carrier-protein] reductase / Acyl carrier protein
Similarity search - Component
Biological speciesHelicobacter pylori (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.38 Å
AuthorsZhou, J.S. / Zhang, L.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)22077081 China
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2023
Title: The Molecular Basis of Catalysis by SDR Family Members Ketoacyl-ACP Reductase FabG and Enoyl-ACP Reductase FabI in Type-II Fatty Acid Biosynthesis.
Authors: Zhou, J. / Zhang, L. / Wang, Y. / Song, W. / Huang, Y. / Mu, Y. / Schmitz, W. / Zhang, S.Y. / Lin, H. / Chen, H.Z. / Ye, F. / Zhang, L.
History
DepositionMay 18, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 15, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Database references / Category: citation / Item: _citation.journal_volume

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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: Acyl carrier protein
H: Acyl carrier protein
I: Acyl carrier protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)190,32416
Polymers185,3659
Non-polymers4,9597
Water1,51384
1
A: 3-oxoacyl-[acyl-carrier-protein] reductase
B: 3-oxoacyl-[acyl-carrier-protein] reductase
G: Acyl carrier protein
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)127,54712
Polymers123,5776
Non-polymers3,9716
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_455-x-1,y,-z+1/21
2
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
H: Acyl carrier protein
I: Acyl carrier protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)126,55010
Polymers123,5776
Non-polymers2,9744
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)85.843, 252.650, 166.440
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

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


Mass: 26768.533 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Helicobacter pylori (bacteria) / Gene: fabG, HPPN135_02765 / Production host: Escherichia coli (E. coli)
References: UniProt: G2M827, 3-oxoacyl-[acyl-carrier-protein] reductase
#2: Protein Acyl carrier protein


Mass: 8251.207 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Helicobacter pylori (bacteria) / Gene: acpP / Production host: Escherichia coli (E. coli) / References: UniProt: Q5EDC8
#3: Chemical
ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C21H28N7O17P3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-UHC / ~{S}-[2-[3-[[(2~{S})-3,3-dimethyl-2-oxidanyl-4-phosphonooxy-butanoyl]amino]propanoylamino]ethyl] 3-oxidanylideneoctanethioate


Mass: 498.528 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H35N2O9PS
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 84 / 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: 2.43 Å3/Da / Density % sol: 49.4 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / Details: 0.2 M Imidazole pH 7.0, 30% v/v MPD

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9875 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 13, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9875 Å / Relative weight: 1
ReflectionResolution: 2.38→126.33 Å / Num. obs: 117507 / % possible obs: 91.4 % / Redundancy: 11 % / CC1/2: 0.997 / Rmerge(I) obs: 0.173 / Net I/σ(I): 10.6
Reflection shellResolution: 2.38→2.56 Å / Rmerge(I) obs: 1.748 / Num. unique obs: 40240 / CC1/2: 0.457

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 8JFH

8jfh


Resolution: 2.38→63.16 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 28.8 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2252 2019 5.02 %
Rwork0.2064 --
obs0.2073 40191 55.35 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.38→63.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11522 0 317 84 11923
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01312002
X-RAY DIFFRACTIONf_angle_d1.45816194
X-RAY DIFFRACTIONf_dihedral_angle_d15.0844315
X-RAY DIFFRACTIONf_chiral_restr0.0831858
X-RAY DIFFRACTIONf_plane_restr0.0082029
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.38-2.440.412480.3051211X-RAY DIFFRACTION4
2.44-2.510.3429250.3505539X-RAY DIFFRACTION11
2.51-2.580.3684450.3553833X-RAY DIFFRACTION17
2.58-2.660.3179690.36031114X-RAY DIFFRACTION23
2.67-2.760.3407580.34791310X-RAY DIFFRACTION30
2.76-2.870.3358970.31841848X-RAY DIFFRACTION38
2.87-30.27341330.32512144X-RAY DIFFRACTION44
3-3.160.30551260.28882664X-RAY DIFFRACTION54
3.16-3.360.28711860.26393209X-RAY DIFFRACTION66
3.36-3.620.25452300.21554284X-RAY DIFFRACTION87
3.62-3.980.21892480.18934898X-RAY DIFFRACTION100
3.98-4.560.16432810.16234938X-RAY DIFFRACTION100
4.56-5.740.20172480.17385029X-RAY DIFFRACTION100
5.74-63.160.21782650.20045151X-RAY DIFFRACTION99

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