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- PDB-5lb9: Structure of the T175V Etr1p mutant in the monoclinic form P21 -

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Basic information

Entry
Database: PDB / ID: 5lb9
TitleStructure of the T175V Etr1p mutant in the monoclinic form P21
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
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: 2.1 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 15, 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)86,78825
Polymers84,1742
Non-polymers2,61423
Water9,314517
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7830 Å2
ΔGint-259 kcal/mol
Surface area31210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.416, 101.861, 81.593
Angle α, β, γ (deg.)90.00, 101.01, 90.00
Int Tables number4
Space group name H-MP1211

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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, 540 molecules

#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 517 / 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: 3.27 Å3/Da / Density % sol: 62.42 % / Description: Rod shape crystal of 500 micron length
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 1.85 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 1.85 M (NH4)2SO4, 100 mM ADA pH 6.4 using streak seeding
PH range: 6.2 -6.5 / Temp details: Appeared at room temperature about 298 K

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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: 2.1→49.47 Å / Num. obs: 60612 / % possible obs: 96.2 % / Redundancy: 3.3 % / CC1/2: 0.996 / Rmerge(I) obs: 0.059 / Rsym value: 0.039 / Net I/σ(I): 11.8
Reflection shellResolution: 2.1→2.21 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.43 / Mean I/σ(I) obs: 2.5 / % possible all: 91.5

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Processing

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

4w99


Resolution: 2.1→42.977 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.9
RfactorNum. reflection% reflection
Rfree0.1859 2979 4.92 %
Rwork0.152 --
obs0.1537 60552 95.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.1→42.977 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5596 0 152 517 6265
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0085883
X-RAY DIFFRACTIONf_angle_d0.8938010
X-RAY DIFFRACTIONf_dihedral_angle_d15.1673473
X-RAY DIFFRACTIONf_chiral_restr0.054910
X-RAY DIFFRACTIONf_plane_restr0.0071019
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.13440.40331110.42592610X-RAY DIFFRACTION91
2.1344-2.17120.35841110.32812584X-RAY DIFFRACTION90
2.1712-2.21070.31041370.23312640X-RAY DIFFRACTION92
2.2107-2.25320.24481620.2052639X-RAY DIFFRACTION93
2.2532-2.29920.23451320.1952611X-RAY DIFFRACTION93
2.2992-2.34920.21451410.19082686X-RAY DIFFRACTION94
2.3492-2.40390.21781330.18152736X-RAY DIFFRACTION95
2.4039-2.4640.23821400.16822702X-RAY DIFFRACTION95
2.464-2.53060.19541440.15982746X-RAY DIFFRACTION97
2.5306-2.6050.20081490.15452800X-RAY DIFFRACTION98
2.605-2.68910.18081590.14782749X-RAY DIFFRACTION98
2.6891-2.78520.20581440.15372801X-RAY DIFFRACTION98
2.7852-2.89670.18431650.15662794X-RAY DIFFRACTION98
2.8967-3.02850.18541500.15772738X-RAY DIFFRACTION97
3.0285-3.18810.19491380.14652817X-RAY DIFFRACTION98
3.1881-3.38780.17471600.14612792X-RAY DIFFRACTION98
3.3878-3.64920.15811400.13682790X-RAY DIFFRACTION98
3.6492-4.01620.18041520.1292786X-RAY DIFFRACTION97
4.0162-4.59680.14261480.11152794X-RAY DIFFRACTION97
4.5968-5.78930.14971220.12072873X-RAY DIFFRACTION99
5.7893-42.98610.17561410.16392885X-RAY DIFFRACTION98
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)
13.0393-0.37220.24113.0945-0.78751.4137-0.2117-0.29270.6460.74520.10150.2386-0.68150.0080.11110.6690.0053-0.09960.3127-0.03210.4541-7.6876111.574556.9664
21.05750.02640.52221.05170.09542.5204-0.0236-0.11460.0990.2214-0.0111-0.0452-0.0566-0.05020.02120.2042-0.0036-0.03030.17230.03850.2413-8.362795.435641.8852
33.0789-0.96890.20661.6560.26262.8205-0.06370.0941-0.07910.01440.0525-0.11590.0376-0.04780.00960.1756-0.0090.00290.16850.00010.1954-17.095892.177121.5917
42.2599-0.11950.84274.38430.22872.1040.12580.29980.25150.0288-0.188-0.69420.03510.3125-0.00330.32760.0445-0.02040.37060.12060.2984-2.310799.05645.3723
51.3886-0.18-0.41061.13090.49691.4626-0.00570.1012-0.2402-0.03390.038-0.06460.2464-0.0312-0.03790.2551-0.0073-0.01870.1907-0.00560.2441-45.104783.18-3.2079
63.71860.1042-0.32763.2392-0.74062.96050.0018-0.23470.45690.0984-0.01130.1565-0.316-0.01710.03170.19030.0128-0.00070.1921-0.05120.2083-41.3764109.48218.8576
75.03540.36951.49246.20450.83742.6241-0.09150.19480.3702-0.2105-0.0153-0.3569-0.14020.26260.06120.16720.00140.00630.21130.00730.2156-28.4893104.63418.6721
80.6768-0.12510.4980.45290.35671.11790.01030.0209-0.0172-0.0709-0.0121-0.0005-0.0230.0128-0.01130.2211-0.00540.01270.18420.01070.2494-42.219294.20964.9978
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 22 through 68 )
2X-RAY DIFFRACTION2chain 'A' and (resid 69 through 250 )
3X-RAY DIFFRACTION3chain 'A' and (resid 251 through 330 )
4X-RAY DIFFRACTION4chain 'A' and (resid 331 through 386 )
5X-RAY DIFFRACTION5chain 'B' and (resid 23 through 181 )
6X-RAY DIFFRACTION6chain 'B' and (resid 182 through 276 )
7X-RAY DIFFRACTION7chain 'B' and (resid 277 through 307 )
8X-RAY DIFFRACTION8chain 'B' and (resid 308 through 386 )

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