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- PDB-1ps9: The Crystal Structure and Reaction Mechanism of E. coli 2,4-Dieno... -

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Basic information

Entry
Database: PDB / ID: 1ps9
TitleThe Crystal Structure and Reaction Mechanism of E. coli 2,4-Dienoyl CoA Reductase
Components2,4-dienoyl-CoA reductase
KeywordsOXIDOREDUCTASE / IRON-SULFUR / TIM BARREL / FLAVODOXIN / FLAVIN / ELECTRON TRANSFER / HYDRIDE TRANSFER
Function / homology
Function and homology information


2,4-dienoyl-CoA reductase [(2E)-enoyl-CoA-producing] / fatty acid beta-oxidation, unsaturated, even number, reductase/isomerase pathway / 2,4-dienoyl-CoA reductase (NADPH) activity / FAD binding / FMN binding / 4 iron, 4 sulfur cluster binding / metal ion binding
Similarity search - Function
NADH:flavin oxidoreductase/NADH oxidase, N-terminal / NADH:flavin oxidoreductase / NADH oxidase family / FAD/NAD(P)-binding domain / Pyridine nucleotide-disulphide oxidoreductase / FAD/NAD(P)-binding domain / FAD/NAD(P)-binding domain / 3-Layer(bba) Sandwich / FAD/NAD(P)-binding domain superfamily / Aldolase class I / Aldolase-type TIM barrel ...NADH:flavin oxidoreductase/NADH oxidase, N-terminal / NADH:flavin oxidoreductase / NADH oxidase family / FAD/NAD(P)-binding domain / Pyridine nucleotide-disulphide oxidoreductase / FAD/NAD(P)-binding domain / FAD/NAD(P)-binding domain / 3-Layer(bba) Sandwich / FAD/NAD(P)-binding domain superfamily / Aldolase class I / Aldolase-type TIM barrel / NAD(P)-binding Rossmann-like Domain / TIM Barrel / Alpha-Beta Barrel / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / FLAVIN MONONUCLEOTIDE / 5-MERCAPTOETHANOL-2-DECENOYL-COENZYME A / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / IRON/SULFUR CLUSTER / 2,4-dienoyl-CoA reductase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.2 Å
AuthorsHubbard, P.A. / Liang, X. / Schulz, H. / Kim, J.J.
Citation
Journal: J.Biol.Chem. / Year: 2003
Title: The crystal structure and reaction mechanism of Escherichia coli 2,4-dienoyl-CoA reductase
Authors: Hubbard, P.A. / Liang, X. / Schulz, H. / Kim, J.J.
#1: Journal: Eur.J.Biochem. / Year: 1997
Title: Cloning and expression of the fadH gene and characterization of the gene product 2,4-dienoyl coenzyme A reductase from Escherichia coli
Authors: He, X.-Y. / Yang, S.-Y. / Schulz, H.
History
DepositionJun 20, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 30, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 31, 2018Group: Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 1.4Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 2,4-dienoyl-CoA reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,0669
Polymers72,6281
Non-polymers3,4388
Water6,720373
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)65.601, 109.227, 110.304
Angle α, β, γ (deg.)90, 90, 90
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein 2,4-dienoyl-CoA reductase / 2 / 4-dienoyl coenzyme A reductase


Mass: 72627.719 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: FADH / Plasmid: pND-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS
References: UniProt: P42593, 2,4-dienoyl-CoA reductase [(2E)-enoyl-CoA-producing]

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Non-polymers , 7 types, 381 molecules

#2: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER / Iron–sulfur cluster


Mass: 351.640 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe4S4
#4: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE / Flavin adenine dinucleotide


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#5: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE / Flavin mononucleotide


Mass: 456.344 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H21N4O9P
#6: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE / Nicotinamide adenine dinucleotide phosphate


Mass: 743.405 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#7: Chemical ChemComp-MDE / 5-MERCAPTOETHANOL-2-DECENOYL-COENZYME A


Mass: 994.877 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C33H55N7O18P3S2
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 373 / 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: 2.72 Å3/Da / Density % sol: 54.77 %
Crystal growTemperature: 292.5 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: PEG 5000, sodium acetate, ammonium sulfate, MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 19.5K
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
130 %PEG5000 MME1reservoir
20.2 Msodium acetate1reservoir
30.1 Mammonium sulfate1reservoir
40.1 MMOPS1reservoirpH6.5
518 %PEG5000 MME1drop
6180 mMsodium acetate1drop
790 mMammonium sulfate1drop
890 mMMOPS1droppH6.5
915 mg/mlprotein1drop

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
Diffraction source
SourceSiteBeamlineTypeIDWavelength (Å)
ROTATING ANODERIGAKU RU20011.5418
SYNCHROTRONAPS 14-BM-C20.9
Detector
TypeIDDetectorDateDetails
RIGAKU RAXIS IIC1IMAGE PLATEAug 21, 2002mirrors
ADSC QUANTUM 42CCDAug 22, 2002mirrors
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Osmic blue confocal mirrorsSINGLE WAVELENGTHMx-ray1
2bent conical Si-mirror (Rh coating), bent cylindrical Ge(111) monochromatorSINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
11.54181
20.91
ReflectionResolution: 2.2→30 Å / Num. obs: 74790 / % possible obs: 94.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 21.1 % / Biso Wilson estimate: 35.1 Å2 / Rmerge(I) obs: 0.057 / Rsym value: 0.057 / Net I/σ(I): 30.3
Reflection shellResolution: 2.2→2.26 Å / Rmerge(I) obs: 0.249 / Mean I/σ(I) obs: 7.8 / Num. unique all: 2553 / Rsym value: 0.249 / % possible all: 61.2
Reflection
*PLUS
Num. obs: 42467 / Num. measured all: 898148
Reflection shell
*PLUS
% possible obs: 61.2 %

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
SHARPphasing
CNSrefinement
RefinementMethod to determine structure: MAD / Resolution: 2.2→30 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.243 3556 -RANDOM
Rwork0.203 ---
all0.205 72563 --
obs0.205 72563 93.7 %-
Displacement parametersBiso mean: 39.5 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.342 Å0.278 Å
Luzzati d res low-5 Å
Luzzati sigma a0.296 Å0.278 Å
Refinement stepCycle: LAST / Resolution: 2.2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5097 0 206 373 5676
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.011
X-RAY DIFFRACTIONc_angle_deg1.416
X-RAY DIFFRACTIONc_dihedral_angle_d22.666
X-RAY DIFFRACTIONc_improper_angle_d5.923
LS refinement shellResolution: 2.2→2.28 Å
RfactorNum. reflection% reflection
Rfree0.309 235 -
Rwork0.304 --
obs-5495 70.8 %
Refinement
*PLUS
Rfactor Rfree: 0.244
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.666
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg5.923

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