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- PDB-8jf9: Crystal structure of 3-oxoacyl-ACP reductase FabG from Helicobact... -

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Basic information

Entry
Database: PDB / ID: 8jf9
TitleCrystal structure of 3-oxoacyl-ACP reductase FabG from Helicobacter pylori
Components3-oxoacyl-[acyl-carrier-protein] reductase
KeywordsBIOSYNTHETIC PROTEIN / 3-oxoacyl-ACP reductase / FabG / 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
3-oxoacyl-[acyl-carrier-protein] reductase
Similarity search - Component
Biological speciesHelicobacter pylori (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 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


Theoretical massNumber of molelcules
Total (without water)107,0744
Polymers107,0744
Non-polymers00
Water17,997999
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13120 Å2
ΔGint-92 kcal/mol
Surface area31090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.770, 113.925, 129.858
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121

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Components

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


Mass: 26768.533 Da / Num. of mol.: 4
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 999 / 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: 2.44 Å3/Da / Density % sol: 49.68 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / Details: 0.1 M NaCl, 15% w/v PEG 6000

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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: 1.9→50 Å / Num. obs: 82455 / % possible obs: 99.7 % / Redundancy: 12.8 % / CC1/2: 0.994 / CC star: 0.999 / Rmerge(I) obs: 0.24 / Rpim(I) all: 0.069 / Rrim(I) all: 0.25 / Χ2: 0.89 / Net I/σ(I): 3.6 / Num. measured all: 1058084
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
1.9-1.9712.52.39581720.7190.9150.6922.4941.003100
1.97-2.0511.91.68781120.8320.9530.5031.7630.4899.7
2.05-2.1412.91.18981890.8610.9620.3411.2380.49999.8
2.14-2.2513.21.33581300.8910.9710.3751.3871.91199.7
2.25-2.39130.84282230.9630.9910.240.8760.65799.7
2.39-2.5812.40.38381950.9770.9940.1120.3990.57899.8
2.58-2.8413.50.26282380.9890.9970.0730.2720.6199.8
2.84-3.2512.70.16482590.9930.9980.0470.1710.70999.5
3.25-4.0913.60.12583450.9960.9990.0350.131.17499.8
4.09-5012.60.08885920.9890.9970.0260.0921.19799

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Processing

Software
NameVersionClassification
PHENIX(1.18.2_3874: ???)refinement
HKL-3000data scaling
HKL-3000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6UUT

6uut


Resolution: 1.9→29.74 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 22.99 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2204 3645 5.13 %
Rwork0.1773 --
obs0.1796 71001 85.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.9→29.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7102 0 0 999 8101
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.017260
X-RAY DIFFRACTIONf_angle_d1.1629775
X-RAY DIFFRACTIONf_dihedral_angle_d17.6322651
X-RAY DIFFRACTIONf_chiral_restr0.0731118
X-RAY DIFFRACTIONf_plane_restr0.0081257
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.930.5353480.4467961X-RAY DIFFRACTION32
1.93-1.960.3525750.31451223X-RAY DIFFRACTION41
1.96-1.980.256980.22371431X-RAY DIFFRACTION49
1.98-2.010.2567780.21951702X-RAY DIFFRACTION56
2.01-2.040.2772950.19711888X-RAY DIFFRACTION63
2.04-2.080.25681090.20562069X-RAY DIFFRACTION69
2.08-2.110.25181290.21862379X-RAY DIFFRACTION79
2.11-2.150.23991300.21662606X-RAY DIFFRACTION87
2.15-2.190.25241380.20522759X-RAY DIFFRACTION92
2.19-2.240.2931280.28542536X-RAY DIFFRACTION84
2.24-2.290.49981220.34982429X-RAY DIFFRACTION81
2.29-2.340.24911490.18572980X-RAY DIFFRACTION99
2.34-2.40.23011690.18172984X-RAY DIFFRACTION99
2.4-2.460.24241710.18622955X-RAY DIFFRACTION99
2.46-2.540.25061450.18083011X-RAY DIFFRACTION99
2.54-2.620.25051660.17542981X-RAY DIFFRACTION100
2.62-2.710.22221440.17743033X-RAY DIFFRACTION100
2.71-2.820.22471820.1762978X-RAY DIFFRACTION100
2.82-2.950.19841580.16793028X-RAY DIFFRACTION100
2.95-3.10.21481650.16993015X-RAY DIFFRACTION100
3.1-3.30.22071830.162985X-RAY DIFFRACTION99
3.3-3.550.19671880.14823041X-RAY DIFFRACTION100
3.55-3.910.17261580.14413031X-RAY DIFFRACTION99
3.91-4.470.17681680.13133062X-RAY DIFFRACTION99
4.47-5.630.17181710.13983084X-RAY DIFFRACTION99
5.63-29.740.18431780.18053205X-RAY DIFFRACTION99

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