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- PDB-4was: STRUCTURE OF THE ETR1P/NADP/CROTONYL-COA COMPLEX -

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Basic information

Entry
Database: PDB / ID: 4was
TitleSTRUCTURE OF THE ETR1P/NADP/CROTONYL-COA COMPLEX
ComponentsEnoyl-[acyl-carrier-protein] reductase [NADPH, B-specific] 1, mitochondrial
KeywordsOXIDOREDUCTASE / MITOCHONDRIAL FATTY ACID SYNTHESIS
Function / homology
Function and homology information


enoyl-[acyl-carrier-protein] reductase (NADPH) / trans-2-enoyl-CoA 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 / Polyketide synthase, enoylreductase domain / Enoylreductase / GroES-like superfamily / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Alpha-Beta Complex ...Quinone Oxidoreductase; Chain A, domain 1 / Medium-chain alcohol dehydrogenases, catalytic domain / Alcohol dehydrogenase-like, C-terminal / Zinc-binding dehydrogenase / 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: 1.7 Å
AuthorsQuade, N. / Voegeli, B. / Rosenthal, R. / Capitani, G. / Erb, T.J.
CitationJournal: Nat.Chem.Biol. / Year: 2015
Title: The use of ene adducts to study and engineer enoyl-thioester reductases.
Authors: Rosenthal, R.G. / Vogeli, B. / Quade, N. / Capitani, G. / Kiefer, P. / Vorholt, J.A. / Ebert, M.O. / Erb, T.J.
History
DepositionAug 31, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Mar 18, 2015Provider: repository / Type: Initial release
Revision 1.1Apr 15, 2015Group: Database references
Revision 1.2Apr 22, 2015Group: Database references
Revision 1.3May 27, 2015Group: Database references
Revision 2.0Jan 10, 2024Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Refinement description
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _atom_site.occupancy / _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
C: Enoyl-[acyl-carrier-protein] reductase [NADPH, B-specific] 1, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)123,4039
Polymers118,6663
Non-polymers4,7376
Water8,701483
1
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)82,2696
Polymers79,1112
Non-polymers3,1584
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6730 Å2
ΔGint-30 kcal/mol
Surface area29170 Å2
MethodPISA
2
C: Enoyl-[acyl-carrier-protein] reductase [NADPH, B-specific] 1, mitochondrial
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)82,2696
Polymers79,1112
Non-polymers3,1584
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area6010 Å2
ΔGint-19 kcal/mol
Surface area29250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)147.920, 106.140, 94.410
Angle α, β, γ (deg.)90.00, 98.41, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11C-523-

HOH

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Components

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


Mass: 39555.402 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Candida tropicalis (yeast) / Gene: ETR1 / Plasmid: pt7-7 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q8WZM3, EC: 1.3.1.10, trans-2-enoyl-CoA reductase (NADPH)
#2: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE / Nicotinamide adenine dinucleotide phosphate


Mass: 743.405 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#3: Chemical ChemComp-COO / CROTONYL COENZYME A


Mass: 835.608 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C25H40N7O17P3S
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 483 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.09 Å3/Da / Density % sol: 60.18 %
Crystal growTemperature: 292 K / Method: vapor diffusion / pH: 7 / Details: 2M ammonium sulfate, 0.1M ADA/NaOH pH 7

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 22, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. obs: 156706 / % possible obs: 99 % / Redundancy: 3.1 % / Rsym value: 0.048 / Net I/σ(I): 10.6
Reflection shellResolution: 1.7→1.9 Å / Redundancy: 3.03 % / Mean I/σ(I) obs: 1 / Rsym value: 1.112 / % possible all: 98.9

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.9_1692) / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1N9G

1n9g


Resolution: 1.7→37.815 Å / SU ML: 0.32 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 33.09 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2242 1097 70 %RANDOM SELECTION
Rwork0.1879 ---
obs0.1882 156656 99.03 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.7→37.815 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8364 0 218 483 9065
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0088802
X-RAY DIFFRACTIONf_angle_d1.17811998
X-RAY DIFFRACTIONf_dihedral_angle_d12.1873163
X-RAY DIFFRACTIONf_chiral_restr0.0481348
X-RAY DIFFRACTIONf_plane_restr0.0061538
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.77740.49321360.430919382X-RAY DIFFRACTION99
1.7774-1.87110.37131370.370719359X-RAY DIFFRACTION99
1.8711-1.98830.34951370.270319390X-RAY DIFFRACTION99
1.9883-2.14180.25831370.223719450X-RAY DIFFRACTION99
2.1418-2.35730.24351370.196619454X-RAY DIFFRACTION99
2.3573-2.69830.24191370.193219518X-RAY DIFFRACTION99
2.6983-3.39930.22641380.191119517X-RAY DIFFRACTION99
3.3993-37.82450.18231380.150719489X-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)
10.3117-0.3543-0.2210.95920.42260.9114-0.0496-0.08160.02650.0596-0.0027-0.058-0.0021-0.0318-00.28040.0429-0.0020.40570.01070.3345-49.43798.306824.4833
20.03850.129-0.07830.23930.171.7987-0.01460.05740.02720.01610.0318-0.00420.47510.090600.42980.0803-0.00490.39440.00090.3449-51.5848.511-21.7864
31.217-0.18770.45970.3097-0.29920.8193-0.0867-0.26340.15590.2376-0.013-0.0465-0.2993-0.0417-00.431-0.012-0.03890.2989-0.06050.3542-0.45330.791823.0598
40.0132-0.01260.00120.00380.00750.0004-0.028-0.0982-0.12910.0527-0.1225-0.32270.00720.0951-0.00020.34860.05670.04540.56220.04270.5166-41.238.038319.7992
5-0.00020.0097-0.00020.01580.00740.00650.23540.18860.193-0.0432-0.1481-0.07040.27880.2236-0.00040.41220.1240.03810.61460.03250.4777-44.681613.367-17.8644
60.0030.0197-0.00070.0085-0.0152-0.0062-0.0258-0.2017-0.04180.01650.00530.14260.0485-0.0534-0.00040.46510.00110.00280.3457-0.02620.48-3.2279-7.500119.0665
70.0115-0.0108-0.0060.01980.01750.0122-0.23190.11220.3875-0.2147-0.10470.0202-0.18130.1079-0.00041.0163-0.03580.08290.94280.14640.8014-44.138116.560613.868
80.0155-0.00380.01570.02620.01990.01630.14790.17390.2319-0.25850.3103-0.6962-0.31570.4585-0.00031.00040.02760.01791.0784-0.09460.8341-40.32037.1269-16.9419
92.05412.09352.01312.16371.95692.2664-0.60140.30170.2143-0.691-0.12020.7978-0.4443-0.1720.76030.7761-0.0754-0.10451.0487-0.00470.93244.2624-4.058917.0309
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain B
3X-RAY DIFFRACTION3chain C
4X-RAY DIFFRACTION4chain D and resid 1
5X-RAY DIFFRACTION5chain D and resid 2
6X-RAY DIFFRACTION6chain D and resid 3
7X-RAY DIFFRACTION7chain E and resid 1
8X-RAY DIFFRACTION8chain E and resid 2
9X-RAY DIFFRACTION9chain E and resid 3

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