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- PDB-5lbx: Structure of the T175V Etr1p mutant in the trigonal form P312 in ... -

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Basic information

Entry
Database: PDB / ID: 5lbx
TitleStructure of the T175V Etr1p mutant in the trigonal form P312 in complex with NADP and crotonyl-CoA
ComponentsEnoyl-[acyl-carrier-protein] reductase [NADPH, B-specific] 1, mitochondrial
KeywordsOXIDOREDUCTASE / Negative catalysis / enzyme / NADP / mitochondria / mutant / crotonyl-coa / reductase
Function / homology
Function and homology information


trans-2-enoyl-CoA reductase (NADPH) activity / enoyl-[acyl-carrier-protein] reductase (NADPH) / enoyl-[acyl-carrier-protein] reductase (NADPH) activity / fatty acid metabolic process / fatty acid biosynthetic process / mitochondrion
Similarity search - Function
: / Quinone Oxidoreductase; Chain A, domain 1 / Medium-chain alcohol dehydrogenases, catalytic domain / Alcohol dehydrogenase-like, C-terminal / Zinc-binding dehydrogenase / Alcohol dehydrogenase, N-terminal / Alcohol dehydrogenase GroES-like domain / Polyketide synthase, enoylreductase domain / Enoylreductase / GroES-like superfamily ...: / Quinone Oxidoreductase; Chain A, domain 1 / Medium-chain alcohol dehydrogenases, catalytic domain / Alcohol dehydrogenase-like, C-terminal / Zinc-binding dehydrogenase / Alcohol dehydrogenase, N-terminal / Alcohol dehydrogenase GroES-like domain / Polyketide synthase, enoylreductase domain / Enoylreductase / GroES-like superfamily / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Alpha-Beta Complex / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
CROTONYL COENZYME A / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Enoyl-[acyl-carrier-protein] reductase 1, mitochondrial
Similarity search - Component
Biological speciesCandida tropicalis (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsWagner, T. / Rosenthal, R.G. / Voegeli, B. / Shima, S. / Erb, T.J.
CitationJournal: Nat. Chem. Biol. / Year: 2017
Title: A conserved threonine prevents self-intoxication of enoyl-thioester reductases.
Authors: Rosenthal, R.G. / Vogeli, B. / Wagner, T. / Shima, S. / Erb, T.J.
History
DepositionJun 17, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 10, 2017Provider: repository / Type: Initial release
Revision 1.1May 24, 2017Group: Database references
Revision 1.2Jun 28, 2017Group: Database references / Category: citation
Item: _citation.country / _citation.journal_volume ..._citation.country / _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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 [NADPH, B-specific] 1, mitochondrial
B: Enoyl-[acyl-carrier-protein] reductase [NADPH, B-specific] 1, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,61720
Polymers84,1742
Non-polymers4,44218
Water3,405189
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9140 Å2
ΔGint-171 kcal/mol
Surface area31060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.498, 93.498, 231.203
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-411-

CL

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Enoyl-[acyl-carrier-protein] reductase [NADPH, B-specific] 1, mitochondrial / Trans-2-enoyl-CoA reductase 1


Mass: 42087.160 Da / Num. of mol.: 2 / Mutation: T175V
Source method: isolated from a genetically manipulated source
Details: The 20 first residues are not visible in the crystal structure. The sequence corresponds to the fragment 23-386 from the original gene sequence.
Source: (gene. exp.) Candida tropicalis (yeast) / Gene: ETR1 / Plasmid: pTE264
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q8WZM3, EC: 1.3.1.10, trans-2-enoyl-CoA reductase (NADPH)

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Non-polymers , 5 types, 207 molecules

#2: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-COO / CROTONYL COENZYME A


Mass: 835.608 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C25H40N7O17P3S
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 189 / 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: 3.47 Å3/Da / Density % sol: 64.57 %
Description: Crystals are transparent cubic shaped with a volume of approximately 50-100 micron cube
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.4
Details: Etr1p was crystallized at 15 mg/mL with 5 mM NADP and 5 mM of crotonyl-CoA in the gel filtration buffer (100 mM NaCl, 20 mM Tris-HCl pH 7.9). Crystals appeared after several days in 2.0 M ...Details: Etr1p was crystallized at 15 mg/mL with 5 mM NADP and 5 mM of crotonyl-CoA in the gel filtration buffer (100 mM NaCl, 20 mM Tris-HCl pH 7.9). Crystals appeared after several days in 2.0 M (NH4)2SO4, 100 mM ADA/NaOH pH 6.4 at room temperature. The crystals were soaked in a solution containing 30% (v/v) glycerol, 2.0 M (NH4)2SO4, 100 mM ADA pH 6.4 prior to freezing in liquid nitrogen to prevent water-crystal formation.
PH range: 6.2-6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1.73913 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Dec 1, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.73913 Å / Relative weight: 1
ReflectionResolution: 2.5→47.04 Å / Num. obs: 41476 / % possible obs: 100 % / Redundancy: 8.6 % / CC1/2: 0.997 / Rmerge(I) obs: 0.124 / Rsym value: 0.044 / Net I/σ(I): 12.2
Reflection shellResolution: 2.5→2.64 Å / Redundancy: 7.7 % / Rmerge(I) obs: 1.511 / Mean I/σ(I) obs: 1.5 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4W99

4w99


Resolution: 2.5→46.749 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 21.9
RfactorNum. reflection% reflection
Rfree0.2124 1958 4.73 %
Rwork0.182 --
obs0.1835 41370 99.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.5→46.749 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5596 0 224 189 6009
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0075932
X-RAY DIFFRACTIONf_angle_d1.0028096
X-RAY DIFFRACTIONf_dihedral_angle_d15.2163482
X-RAY DIFFRACTIONf_chiral_restr0.054915
X-RAY DIFFRACTIONf_plane_restr0.0071024
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.56250.36281470.34442745X-RAY DIFFRACTION99
2.5625-2.63180.38971570.30542746X-RAY DIFFRACTION100
2.6318-2.70930.29161320.26252784X-RAY DIFFRACTION100
2.7093-2.79670.26541610.23772746X-RAY DIFFRACTION100
2.7967-2.89660.29441190.2292803X-RAY DIFFRACTION100
2.8966-3.01260.22121210.22722810X-RAY DIFFRACTION100
3.0126-3.14970.25841270.22172775X-RAY DIFFRACTION100
3.1497-3.31570.22561230.18522823X-RAY DIFFRACTION100
3.3157-3.52340.21111410.18532811X-RAY DIFFRACTION100
3.5234-3.79530.22121420.17642791X-RAY DIFFRACTION100
3.7953-4.1770.17771400.15292832X-RAY DIFFRACTION100
4.177-4.78090.16321500.13322846X-RAY DIFFRACTION100
4.7809-6.02140.17081500.14412876X-RAY DIFFRACTION100
6.0214-46.75720.19491480.17143024X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.51790.93810.63012.040.23462.0181-0.0020.105-0.3562-0.0390.0361-0.18910.1398-0.0437-0.02840.38150.0097-0.01040.3995-0.01320.4174-15.6321-3.930728.4369
21.9186-0.95720.61122.6075-0.01842.6508-0.1058-0.0811-0.04790.01130.068-0.0025-0.2580.00470.04660.4028-0.02650.00330.3477-0.01750.3633-26.28723.752913.093
30.4905-0.27550.80460.7253-0.65742.5155-0.0165-0.07270.0279-0.00530.06880.0306-0.0165-0.0955-0.080.38470.017-0.0030.3828-0.04250.3952-24.730811.050615.7906
41.7198-1.1823-0.69952.62391.02082.35030.08760.13830.2488-0.338-0.0221-0.1831-0.56490.0495-0.09850.5088-0.0348-0.00730.3204-0.00360.3415-33.936728.8988-35.6323
51.76820.4261-0.02542.127-0.98763.4271-0.0162-0.0099-0.1454-0.03720.037-0.0690.16310.0386-0.02420.3828-0.00080.00760.3635-0.05170.3928-30.6158-0.2081-19.5546
60.2191-0.2850.16520.9348-0.50152.72890.0080.0061-0.06730.0028-0.01290.0365-0.0922-0.00940.00590.4063-0.0446-0.00280.3465-0.04260.4172-33.356912.5164-21.7318
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 22 through 162 )
2X-RAY DIFFRACTION2chain 'A' and (resid 163 through 276 )
3X-RAY DIFFRACTION3chain 'A' and (resid 277 through 386 )
4X-RAY DIFFRACTION4chain 'B' and (resid 22 through 162 )
5X-RAY DIFFRACTION5chain 'B' and (resid 163 through 276 )
6X-RAY DIFFRACTION6chain 'B' and (resid 277 through 386 )

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