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

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Basic information

Entry
Database: PDB / ID: 8jfa
TitleCrystal structure of 3-oxoacyl-ACP reductase FabG in complex with NADPH from Helicobacter pylori
Components3-oxoacyl-[acyl-carrier-protein] reductase
KeywordsBIOSYNTHETIC PROTEIN / 3-oxoacyl-ACP reductase / FabG / NADPH / Helicobacter pylori
Function / homology
Function and homology information


3-oxoacyl-[acyl-carrier-protein] reductase (NADPH) activity / 3-oxoacyl-[acyl-carrier-protein] reductase / NAD binding / fatty acid biosynthetic process
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
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 3-oxoacyl-[acyl-carrier-protein] reductase
Similarity search - Component
Biological speciesHelicobacter pylori (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.55 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 17, 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

Downloads & links

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)164,54912
Polymers160,0896
Non-polymers4,4606
Water905
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)109,6998
Polymers106,7264
Non-polymers2,9744
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17450 Å2
ΔGint-91 kcal/mol
Surface area30780 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)109,6998
Polymers106,7264
Non-polymers2,9744
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area17410 Å2
ΔGint-99 kcal/mol
Surface area30530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)139.093, 79.435, 151.951
Angle α, β, γ (deg.)90.00, 106.92, 90.00
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 26681.455 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: 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
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 5 / 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: 2.51 Å3/Da / Density % sol: 50.96 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / Details: 0.2 M NaCl, 0.1 M MES pH 6.0, 10% w/v PEG 8000

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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: May 13, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9875 Å / Relative weight: 1
ReflectionResolution: 2.55→145.38 Å / Num. obs: 51590 / % possible obs: 99.8 % / Redundancy: 5.3 % / CC1/2: 0.993 / Rmerge(I) obs: 0.108 / Rpim(I) all: 0.051 / Rrim(I) all: 0.12 / Χ2: 0.96 / Net I/σ(I): 8.7 / Num. measured all: 273613
Reflection shellResolution: 2.55→2.69 Å / % possible obs: 100 % / Redundancy: 5.4 % / Rmerge(I) obs: 0.704 / Num. measured all: 40626 / Num. unique obs: 7489 / CC1/2: 0.78 / Rpim(I) all: 0.331 / Rrim(I) all: 0.781 / Χ2: 0.79 / Net I/σ(I) obs: 2.4

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Processing

Software
NameVersionClassification
PHENIX(1.18.2_3874: ???)refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6UUT

6uut


Resolution: 2.55→46.41 Å / SU ML: 0.41 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 33.87 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2714 2535 4.92 %
Rwork0.2346 --
obs0.2365 51571 99.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.55→46.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10638 0 288 5 10931
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0111088
X-RAY DIFFRACTIONf_angle_d1.36314962
X-RAY DIFFRACTIONf_dihedral_angle_d23.123972
X-RAY DIFFRACTIONf_chiral_restr0.0751704
X-RAY DIFFRACTIONf_plane_restr0.0091870
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.55-2.60.35371280.33512722X-RAY DIFFRACTION100
2.6-2.660.39881310.33572732X-RAY DIFFRACTION100
2.66-2.710.38591440.33872701X-RAY DIFFRACTION100
2.71-2.780.40311440.33832724X-RAY DIFFRACTION100
2.78-2.850.40241370.33192690X-RAY DIFFRACTION100
2.85-2.920.37921490.31082691X-RAY DIFFRACTION100
2.92-3.010.38291360.31322734X-RAY DIFFRACTION100
3.01-3.110.31471260.31152721X-RAY DIFFRACTION100
3.11-3.220.3711490.29272718X-RAY DIFFRACTION100
3.22-3.350.35191170.29412751X-RAY DIFFRACTION100
3.35-3.50.33791320.26872718X-RAY DIFFRACTION100
3.5-3.680.29871350.25592719X-RAY DIFFRACTION100
3.68-3.910.24861580.24912714X-RAY DIFFRACTION100
3.91-4.220.25661220.22222771X-RAY DIFFRACTION100
4.22-4.640.23361660.1942693X-RAY DIFFRACTION100
4.64-5.310.23251380.1862732X-RAY DIFFRACTION99
5.31-6.690.24971660.21932726X-RAY DIFFRACTION99
6.69-46.410.20691570.17722779X-RAY DIFFRACTION99

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