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- PDB-8rcz: Structure of the enoyl-ACP reductase FabV from Pseudomonas aerugi... -

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Basic information

Entry
Database: PDB / ID: 8rcz
TitleStructure of the enoyl-ACP reductase FabV from Pseudomonas aeruginosa with NADH cofactor
ComponentsEnoyl-[acyl-carrier-protein] reductase [NADH]
KeywordsOXIDOREDUCTASE / FabV / enoyl-ACP reductase / Pseudomonas aeruginosa / NADH
Function / homology
Function and homology information


trans-2-enoyl-CoA reductase (NADH) activity / enoyl-[acyl-carrier-protein] reductase (NADH) / enoyl-[acyl-carrier-protein] reductase (NADH) activity / NAD binding / fatty acid biosynthetic process
Similarity search - Function
: / Trans-2-enoyl-CoA reductase / Enoyl reductase FAD binding domain / Trans-2-enoyl-CoA reductase catalytic domain, putative / Enoyl reductase FAD binding domain / Trans-2-enoyl-CoA reductase catalytic region / NAD(P)H binding domain of trans-2-enoyl-CoA reductase
Similarity search - Domain/homology
1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / Enoyl-[acyl-carrier-protein] reductase [NADH]
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsVandebroek, L. / Van Olmen, F. / Voet, A.R.D. / Verwilst, P.
Funding support Belgium, 1items
OrganizationGrant numberCountry
Research Foundation - Flanders (FWO)1235722N Belgium
CitationJournal: To Be Published
Title: Structure of the enoyl-ACP reductase FabV from Pseudomonas aeruginosa with NADH cofactor
Authors: Vandebroek, L. / Van Olmen, F. / Voet, A.R.D. / Verwilst, P.
History
DepositionDec 7, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 18, 2024Provider: repository / Type: Initial release

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


Theoretical massNumber of molelcules
Total (without water)89,1204
Polymers87,7892
Non-polymers1,3312
Water2,828157
1
A: Enoyl-[acyl-carrier-protein] reductase [NADH]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,5602
Polymers43,8951
Non-polymers6651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Enoyl-[acyl-carrier-protein] reductase [NADH]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,5602
Polymers43,8951
Non-polymers6651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)54.744, 88.729, 158.172
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 43894.504 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: fabV
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: A0A2R3IT83
#2: Chemical ChemComp-NAI / 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / NADH


Mass: 665.441 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H29N7O14P2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 157 / 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: 2.19 Å3/Da / Density % sol: 43.78 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 8.7
Details: 0.5M lithium chloride, 0.1M Tris pH 8.7, 24% PEG 6000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.873128 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Apr 20, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.873128 Å / Relative weight: 1
ReflectionResolution: 2.25→89.58 Å / Num. obs: 70614 / % possible obs: 96.1 % / Redundancy: 7.2 % / CC1/2: 0.957 / Rmerge(I) obs: 0.1721 / Rpim(I) all: 0.112 / Rrim(I) all: 0.315 / Χ2: 0.96 / Net I/σ(I): 8.9
Reflection shellResolution: 2.45→2.55 Å / % possible obs: 94.7 % / Redundancy: 6.8 % / Rmerge(I) obs: 0.748 / Num. measured all: 21204 / Num. unique obs: 3115 / CC1/2: 0.877 / Rpim(I) all: 0.285 / Rrim(I) all: 0.803 / Χ2: 0.86 / Net I/σ(I) obs: 3.7

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
Aimlessdata scaling
PHASERphasing
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.25→45.01 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 25.47 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2421 3622 5.13 %
Rwork0.1971 --
obs0.1994 70614 99.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.25→45.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5975 0 88 157 6220
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0026184
X-RAY DIFFRACTIONf_angle_d0.5218394
X-RAY DIFFRACTIONf_dihedral_angle_d17.5332251
X-RAY DIFFRACTIONf_chiral_restr0.041939
X-RAY DIFFRACTIONf_plane_restr0.0031082
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.25-2.280.28571250.272697X-RAY DIFFRACTION100
2.28-2.310.27911390.25452525X-RAY DIFFRACTION100
2.31-2.340.26961510.25422535X-RAY DIFFRACTION100
2.34-2.380.31241450.25922615X-RAY DIFFRACTION100
2.38-2.420.3021450.26532547X-RAY DIFFRACTION100
2.42-2.460.31911700.26292522X-RAY DIFFRACTION100
2.46-2.50.30651640.24572567X-RAY DIFFRACTION100
2.5-2.540.27991580.25092550X-RAY DIFFRACTION100
2.54-2.590.30571480.23462572X-RAY DIFFRACTION100
2.59-2.650.24221390.22522536X-RAY DIFFRACTION100
2.65-2.70.28951290.2252613X-RAY DIFFRACTION100
2.7-2.770.27121630.232543X-RAY DIFFRACTION100
2.77-2.830.29041230.2152619X-RAY DIFFRACTION100
2.83-2.910.30891630.22692554X-RAY DIFFRACTION100
2.91-30.27341410.21842559X-RAY DIFFRACTION100
3-3.090.28551690.22292538X-RAY DIFFRACTION100
3.09-3.20.26551230.21222628X-RAY DIFFRACTION100
3.2-3.330.29321050.21112551X-RAY DIFFRACTION100
3.33-3.480.31711090.21012636X-RAY DIFFRACTION100
3.48-3.670.25711400.19432556X-RAY DIFFRACTION100
3.67-3.90.21891500.17442604X-RAY DIFFRACTION100
3.9-4.20.21011150.16222585X-RAY DIFFRACTION100
4.2-4.620.1971210.15792590X-RAY DIFFRACTION100
4.62-5.290.19781300.15562578X-RAY DIFFRACTION100
5.29-6.660.21471260.18882589X-RAY DIFFRACTION100
6.66-45.010.1351310.15462583X-RAY DIFFRACTION100

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