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- PDB-8jfm: Crystal structure of enoyl-ACP reductase FabI in complex with NAD... -

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Basic information

Entry
Database: PDB / ID: 8jfm
TitleCrystal structure of enoyl-ACP reductase FabI in complex with NADH from Helicobacter pylori
ComponentsEnoyl-[acyl-carrier-protein] reductase [NADH]
KeywordsBIOSYNTHETIC PROTEIN / enoyl-ACP reductase / FabI / NADH / Helicobacter pylori
Function / homologyEnoyl-[acyl-carrier-protein] reductase (NADH) / enoyl-[acyl-carrier-protein] reductase (NADH) / Enoyl-(Acyl carrier protein) reductase / Short-chain dehydrogenase/reductase SDR / NAD(P)-binding domain superfamily / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Enoyl-[acyl-carrier-protein] reductase [NADH]
Function and homology information
Biological speciesHelicobacter pylori (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.21 Å
AuthorsSong, W.Y. / 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

Downloads & links

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Assembly

Deposited unit
A: Enoyl-[acyl-carrier-protein] reductase [NADH]
B: Enoyl-[acyl-carrier-protein] reductase [NADH]
C: Enoyl-[acyl-carrier-protein] reductase [NADH]
D: Enoyl-[acyl-carrier-protein] reductase [NADH]
E: Enoyl-[acyl-carrier-protein] reductase [NADH]
F: Enoyl-[acyl-carrier-protein] reductase [NADH]
G: Enoyl-[acyl-carrier-protein] reductase [NADH]
H: Enoyl-[acyl-carrier-protein] reductase [NADH]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)243,27716
Polymers237,9698
Non-polymers5,3078
Water22,0861226
1
A: Enoyl-[acyl-carrier-protein] reductase [NADH]
B: Enoyl-[acyl-carrier-protein] reductase [NADH]
C: Enoyl-[acyl-carrier-protein] reductase [NADH]
D: Enoyl-[acyl-carrier-protein] reductase [NADH]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)121,6388
Polymers118,9854
Non-polymers2,6544
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area21250 Å2
ΔGint-156 kcal/mol
Surface area33670 Å2
MethodPISA
2
E: Enoyl-[acyl-carrier-protein] reductase [NADH]
F: Enoyl-[acyl-carrier-protein] reductase [NADH]
G: Enoyl-[acyl-carrier-protein] reductase [NADH]
H: Enoyl-[acyl-carrier-protein] reductase [NADH]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)121,6388
Polymers118,9854
Non-polymers2,6544
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area21370 Å2
ΔGint-155 kcal/mol
Surface area33570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.808, 110.545, 142.943
Angle α, β, γ (deg.)90.00, 99.12, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Enoyl-[acyl-carrier-protein] reductase [NADH]


Mass: 29746.154 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Helicobacter pylori (bacteria) / Gene: fabI, CGC32_06335, HPF51_0191 / Production host: Escherichia coli (E. coli)
References: UniProt: A0A086RSH0, enoyl-[acyl-carrier-protein] reductase (NADH)
#2: Chemical
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: NAD*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1226 / 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: 2.31 Å3/Da / Density % sol: 46.81 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / Details: 0.2 M ammonium sulfate, 15% w/v PEG 4000

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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: 2.2→50 Å / Num. obs: 103721 / % possible obs: 99.3 % / Redundancy: 4.6 % / CC1/2: 0.948 / CC star: 0.987 / Rmerge(I) obs: 0.168 / Rpim(I) all: 0.086 / Rrim(I) all: 0.189 / Χ2: 1.204 / Net I/σ(I): 3.5 / Num. measured all: 475914
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
2.2-2.284.10.42102930.8790.9670.2360.4840.45599
2.28-2.374.40.431102840.8820.9680.230.4910.46998.9
2.37-2.484.60.412103290.9020.9740.2120.4650.47499.3
2.48-2.614.60.362103150.910.9760.1850.4080.49699.3
2.61-2.774.40.295102580.930.9820.1550.3350.55998.5
2.77-2.994.90.239103900.9580.9890.1190.2680.65599.5
2.99-3.294.90.175103930.9730.9930.0880.1960.84499.9
3.29-3.764.70.134104540.9740.9930.0690.1511.31599.8
3.76-4.744.60.106104200.9790.9950.0550.122.02199.3
4.74-504.70.115105850.9660.9910.0580.134.43799.7

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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: 8JFJ

8jfj


Resolution: 2.21→46.47 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 20.24 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2053 5203 5.03 %
Rwork0.1526 --
obs0.1553 103454 93.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.21→46.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16766 0 0 1226 17992
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00717099
X-RAY DIFFRACTIONf_angle_d0.99723183
X-RAY DIFFRACTIONf_dihedral_angle_d9.7432335
X-RAY DIFFRACTIONf_chiral_restr0.0572685
X-RAY DIFFRACTIONf_plane_restr0.0062861
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.21-2.230.2785600.1652931X-RAY DIFFRACTION27
2.23-2.260.2216750.17151834X-RAY DIFFRACTION53
2.26-2.290.24131290.16842453X-RAY DIFFRACTION71
2.29-2.320.25891620.17132975X-RAY DIFFRACTION85
2.32-2.350.24991840.16283331X-RAY DIFFRACTION96
2.35-2.380.2141770.16133447X-RAY DIFFRACTION99
2.38-2.410.2211900.15363425X-RAY DIFFRACTION99
2.41-2.450.21411830.15463483X-RAY DIFFRACTION99
2.45-2.490.24681930.15923455X-RAY DIFFRACTION100
2.49-2.530.21751870.15893405X-RAY DIFFRACTION99
2.53-2.570.21761820.16393509X-RAY DIFFRACTION99
2.57-2.620.22841880.15773457X-RAY DIFFRACTION100
2.62-2.670.20851890.1593455X-RAY DIFFRACTION99
2.67-2.720.23111700.15953443X-RAY DIFFRACTION99
2.72-2.780.21921900.16353478X-RAY DIFFRACTION99
2.78-2.850.22751620.16313379X-RAY DIFFRACTION97
2.85-2.920.22212100.16453471X-RAY DIFFRACTION100
2.92-30.2361760.16423512X-RAY DIFFRACTION100
3-3.090.23441730.16193441X-RAY DIFFRACTION100
3.09-3.190.1881830.15343503X-RAY DIFFRACTION100
3.19-3.30.20771720.15343501X-RAY DIFFRACTION100
3.3-3.430.19262030.14673505X-RAY DIFFRACTION100
3.43-3.590.19061830.15123483X-RAY DIFFRACTION100
3.59-3.780.1911790.14963522X-RAY DIFFRACTION100
3.78-4.010.19781900.13513476X-RAY DIFFRACTION100
4.01-4.320.16991710.12953447X-RAY DIFFRACTION98
4.32-4.760.161780.13053516X-RAY DIFFRACTION100
4.76-5.450.18131790.14233513X-RAY DIFFRACTION100
5.45-6.860.23081940.17183512X-RAY DIFFRACTION100
6.86-46.470.19051910.15983389X-RAY DIFFRACTION94

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