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

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Basic information

Entry
Database: PDB / ID: 8jfn
TitleCrystal structure of enoyl-ACP reductase FabI in complex with NAD+ and crotonyl-ACP from Helicobacter pylori
Components
  • Acyl carrier protein
  • Enoyl-[acyl-carrier-protein] reductase [NADH]
KeywordsBIOSYNTHETIC PROTEIN / enoyl-ACP reductase / FabI / NAD+ / crotonyl-ACP / Helicobacter pylori
Function / homology
Function and homology information


Kdo2-lipid A biosynthetic process / enoyl-[acyl-carrier-protein] reductase (NADH) / enoyl-[acyl-carrier-protein] reductase (NADH) activity / lipid A biosynthetic process / acyl binding / acyl carrier activity / phosphopantetheine binding / fatty acid biosynthetic process / membrane / cytosol
Similarity search - Function
Enoyl-[acyl-carrier-protein] reductase (NADH) / Polyketide synthase, phosphopantetheine-binding domain / Phosphopantetheine attachment site / 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 ...Enoyl-[acyl-carrier-protein] reductase (NADH) / Polyketide synthase, phosphopantetheine-binding domain / Phosphopantetheine attachment site / 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
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Chem-PSR / Enoyl-[acyl-carrier-protein] reductase [NADH] / Acyl carrier protein
Similarity search - Component
Biological speciesHelicobacter pylori (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.41 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
Revision 1.2Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Enoyl-[acyl-carrier-protein] reductase [NADH]
B: Acyl carrier protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,5794
Polymers38,4872
Non-polymers1,0922
Water1,74797
1
A: Enoyl-[acyl-carrier-protein] reductase [NADH]
B: Acyl carrier protein
hetero molecules

A: Enoyl-[acyl-carrier-protein] reductase [NADH]
B: Acyl carrier protein
hetero molecules

A: Enoyl-[acyl-carrier-protein] reductase [NADH]
B: Acyl carrier protein
hetero molecules

A: Enoyl-[acyl-carrier-protein] reductase [NADH]
B: Acyl carrier protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)158,31516
Polymers153,9488
Non-polymers4,3678
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_445-x-1,-y-1,z1
crystal symmetry operation3_455-x-1,y,-z1
crystal symmetry operation4_545x,-y-1,-z1
Buried area29520 Å2
ΔGint-169 kcal/mol
Surface area47720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.272, 101.816, 126.329
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-408-

HOH

21A-432-

HOH

31A-472-

HOH

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Components

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


Mass: 29746.154 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Helicobacter pylori (bacteria) / Gene: fabI / Production host: Escherichia coli (E. coli) / References: UniProt: A0A086RSH0
#2: Protein Acyl carrier protein


Mass: 8740.794 Da / Num. of mol.: 1
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-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#4: Chemical ChemComp-PSR / THIOBUTYRIC ACID S-{2-[3-(2-HYDROXY-3,3-DIMETHYL-4-PHOSPHONOOXY-BUTYRYLAMINO)-PROPIONYLAMINO]-ETHYL} ESTER


Mass: 428.438 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H29N2O8PS / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 97 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 3.22 Å3/Da / Density % sol: 61.81 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / Details: 0.2 M sodium citrate pH 5.5, 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: Jun 13, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9875 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 19566 / % possible obs: 99.4 % / Redundancy: 12.1 % / CC1/2: 0.979 / CC star: 0.995 / Rmerge(I) obs: 0.172 / Rpim(I) all: 0.051 / Rrim(I) all: 0.18 / Χ2: 0.987 / Net I/σ(I): 6.2 / Num. measured all: 235980
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
2.4-2.497.70.90618460.8980.9730.3110.9610.93493.8
2.49-2.5910.30.71919070.9670.9910.220.7530.94299.8
2.59-2.711.90.60519360.9790.9950.1770.6310.952100
2.7-2.8512.60.49619480.9830.9960.1430.5170.972100
2.85-3.0213.10.38919500.9880.9970.1110.4050.966100
3.02-3.2612.20.29119490.9860.9970.0880.3050.998100
3.26-3.5813.70.219700.9910.9980.0560.2081.02100
3.58-4.113.50.15319790.9920.9980.0430.1590.97100
4.1-5.1712.40.12419860.9910.9980.0370.130.88100
5.17-5012.70.16320950.9720.9930.0490.171.18100

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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: 8JFM

8jfm


Resolution: 2.41→40.29 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.08 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2353 803 4.9 %
Rwork0.1833 --
obs0.1858 16395 83.3 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.41→40.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2707 0 44 97 2848
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082798
X-RAY DIFFRACTIONf_angle_d1.1193793
X-RAY DIFFRACTIONf_dihedral_angle_d21.36441
X-RAY DIFFRACTIONf_chiral_restr0.057440
X-RAY DIFFRACTIONf_plane_restr0.007477
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.41-2.560.2862670.22811119X-RAY DIFFRACTION37
2.56-2.760.2812910.22581991X-RAY DIFFRACTION64
2.76-3.030.27181860.22212984X-RAY DIFFRACTION98
3.03-3.470.24131470.19923101X-RAY DIFFRACTION100
3.47-4.370.20371530.16833135X-RAY DIFFRACTION100
4.37-40.290.22641590.16053262X-RAY DIFFRACTION100

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