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- PDB-6fn6: Modifying region (DH-ER-KR) of an insect fatty acid synthase (FAS) -

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Basic information

Entry
Database: PDB / ID: 6fn6
TitleModifying region (DH-ER-KR) of an insect fatty acid synthase (FAS)
ComponentsFatty acid synthase 1, isoform A
KeywordsTRANSFERASE / Dehydratase / Enoylreductase / Ketoreductase / lipid metabolism / fatty acid
Function / homology
Function and homology information


: / : / : / : / : / triglyceride biosynthetic process / cellular response to sucrose stimulus / fatty-acid synthase system / enoyl-[acyl-carrier-protein] reductase (NADPH, Re-specific) / [acyl-carrier-protein] S-acetyltransferase activity ...: / : / : / : / : / triglyceride biosynthetic process / cellular response to sucrose stimulus / fatty-acid synthase system / enoyl-[acyl-carrier-protein] reductase (NADPH, Re-specific) / [acyl-carrier-protein] S-acetyltransferase activity / response to sucrose / enoyl-[acyl-carrier-protein] reductase (NADPH) activity / beta-ketoacyl-[acyl-carrier-protein] synthase I / 3-oxoacyl-[acyl-carrier-protein] reductase (NADPH) activity / 3-oxoacyl-[acyl-carrier-protein] reductase / oleoyl-[acyl-carrier-protein] hydrolase / fatty acyl-[ACP] hydrolase activity / fatty acid synthase activity / phosphopantetheine binding / 3-oxoacyl-[acyl-carrier-protein] synthase activity / fatty acid biosynthetic process
Similarity search - Function
Polyketide synthase dehydratase / : / Fatty acid synthase, pseudo-KR domain / Zinc-binding dehydrogenase / Thioesterase / Thioesterase domain / Polyketide synthase, dehydratase domain / PKS_DH / : / Polyketide synthase dehydratase domain ...Polyketide synthase dehydratase / : / Fatty acid synthase, pseudo-KR domain / Zinc-binding dehydrogenase / Thioesterase / Thioesterase domain / Polyketide synthase, dehydratase domain / PKS_DH / : / Polyketide synthase dehydratase domain / : / Polyketide and metazoan fatty acid synthase dehydratase (PKS/mFAS DH) domain profile. / Polyketide synthase, dehydratase domain superfamily / Polyketide synthase, C-terminal extension / Thiol Ester Dehydrase; Chain A / Ketoacyl-synthetase C-terminal extension / Polyketide synthase, ketoreductase domain / KR domain / Malonyl-CoA ACP transacylase, ACP-binding / : / Zinc-binding dehydrogenase / Acyl transferase / Acyl transferase domain / Acyl transferase domain in polyketide synthase (PKS) enzymes. / Acyl transferase domain superfamily / Polyketide synthase, enoylreductase domain / Enoylreductase / Acyl transferase/acyl hydrolase/lysophospholipase / Polyketide synthase, phosphopantetheine-binding domain / Phosphopantetheine attachment site / PKS_KR / Beta-ketoacyl synthase / Beta-ketoacyl synthase, active site / Ketosynthase family 3 (KS3) active site signature. / Ketosynthase family 3 (KS3) domain profile. / Beta-ketoacyl synthase, N-terminal / Beta-ketoacyl synthase, C-terminal / Polyketide synthase, beta-ketoacyl synthase domain / Beta-ketoacyl synthase, N-terminal domain / Beta-ketoacyl synthase, C-terminal domain / GroES-like superfamily / Thiolase-like / Phosphopantetheine attachment site / ACP-like superfamily / Carrier protein (CP) domain profile. / Phosphopantetheine binding ACP domain / Alpha/Beta hydrolase fold / NAD(P)-binding domain superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
BROMIDE ION / Fatty acid synthase
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsBenning, F.M.C. / Bukhari, H.S.T. / Jakob, R.P. / Maier, T.
CitationJournal: To Be Published
Title: Modifying region (DH-ER-KR) of an insect fatty acid synthase (FAS)
Authors: Benning, F.M.C. / Bukhari, H.S.T. / Jakob, R.P. / Maier, T.
History
DepositionFeb 2, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 13, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 17, 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: Fatty acid synthase 1, isoform A
B: Fatty acid synthase 1, isoform A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)259,3567
Polymers259,0102
Non-polymers3465
Water3,513195
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5320 Å2
ΔGint-16 kcal/mol
Surface area91410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.448, 174.149, 194.454
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 Fatty acid synthase 1, isoform A


Mass: 129504.859 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly)
Gene: FASN1, anon-EST:Posey235, anon-EST:Posey43, anon-WO0138581.1, BcDNA:GH07626, BcDNA:gh07626, dFAS, DM_7295848, Dmel\CG3523, FAS, Fas, fas, FAS[CG3523], FASN, FASN[CG3523], Fatty acid synthase, CG3523, Dmel_CG3523
Plasmid: pAB1G
Details (production host): Gateway-compatible pACEBAC plasmid
Cell line (production host): 21 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: Q9VQL7, 3-oxoacyl-[acyl-carrier-protein] reductase, EC: 1.3.1.10, [acyl-carrier-protein] S-acetyltransferase, [acyl-carrier-protein] S-malonyltransferase, beta-ketoacyl-[acyl- ...References: UniProt: Q9VQL7, 3-oxoacyl-[acyl-carrier-protein] reductase, EC: 1.3.1.10, [acyl-carrier-protein] S-acetyltransferase, [acyl-carrier-protein] S-malonyltransferase, beta-ketoacyl-[acyl-carrier-protein] synthase I, fatty-acid synthase system, oleoyl-[acyl-carrier-protein] hydrolase, 3-hydroxyacyl-[acyl-carrier-protein] dehydratase
#2: Chemical ChemComp-BR / BROMIDE ION


Mass: 79.904 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Br
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 195 / 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: 2.47 Å3/Da / Density % sol: 50.12 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1 M Bis-Tris propane pH 6.5, 0.35 M Na Br, 17.5% PEG 3350, 10 mM NADP+

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1.00003 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Feb 8, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00003 Å / Relative weight: 1
ReflectionResolution: 2.7→129.729 Å / Num. obs: 68241 / % possible obs: 96 % / Redundancy: 24.06 % / Biso Wilson estimate: 54.01 Å2 / CC1/2: 0.998 / Rrim(I) all: 0.24 / Net I/σ(I): 15.57
Reflection shellResolution: 2.7→2.797 Å / Redundancy: 20.87 % / Mean I/σ(I) obs: 2.33 / Num. unique obs: 6989 / CC1/2: 0.832 / Rrim(I) all: 1.81 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIXdev_1992refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2vz9

2vz9


Resolution: 2.7→129.729 Å / SU ML: 0.42 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 27.1
RfactorNum. reflection% reflection
Rfree0.2546 3384 4.96 %
Rwork0.2206 --
obs0.2223 68241 95.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.7→129.729 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16905 0 14 198 17117
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00317195
X-RAY DIFFRACTIONf_angle_d0.69223267
X-RAY DIFFRACTIONf_dihedral_angle_d11.7726338
X-RAY DIFFRACTIONf_chiral_restr0.0352711
X-RAY DIFFRACTIONf_plane_restr0.0032985
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)
11.1473-0.22980.33443.10131.04173.2630.16410.16080.0265-0.4204-0.30060.57540.0012-0.32410.08970.40360.0479-0.13370.4793-0.11720.3389-13.3544101.855870.3348
21.87911.2448-0.43791.8144-0.29590.48590.00940.2390.2748-0.2380.09-0.14130.02870.0175-0.05590.4984-0.0068-0.07850.4480.08530.321528.6381143.579868.317
30.41691.13320.38877.074-0.79440.49350.274-0.0538-0.18780.214-0.0046-0.21740.0719-0.0778-0.03050.3859-0.0069-0.11460.52830.04530.43823.8776101.148191.1695
40.79170.49560.23232.60560.77480.50970.1492-0.1733-0.19290.09490.0194-0.48180.1407-0.0528-0.14650.4233-0.0455-0.09340.44440.06870.281615.3086100.744988.4757
52.8248-0.00310.57476.02920.30172.0289-0.06190.1536-0.1994-0.3924-0.0886-0.5836-0.10240.02310.09160.46660.00410.03440.437-0.0230.3026-0.77859.86753.8213
60.94951.3790.17662.7489-0.21130.1068-0.16090.0033-0.024-0.33880.20730.28760.0075-0.0248-0.07160.53930.00080.01830.57190.12780.535-37.471514.336959.9162
70.02642.07570.73935.37472.81261.33710.2897-0.1993-0.22770.1187-0.2882-0.5462-0.00810.12590.0030.6313-0.1362-0.01040.76660.15440.8584-20.202728.144278.4614
80.30280.4515-0.20333.46330.73440.68570.1701-0.176-0.33990.606-0.40290.06810.12190.05350.20150.4998-0.1823-0.17860.66890.16620.6624-9.626147.671785.0692
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 893 through 1125 )
2X-RAY DIFFRACTION2chain 'A' and (resid 1126 through 1432 )
3X-RAY DIFFRACTION3chain 'A' and (resid 1433 through 1586 )
4X-RAY DIFFRACTION4chain 'A' and (resid 1587 through 2031 )
5X-RAY DIFFRACTION5chain 'B' and (resid 893 through 1125 )
6X-RAY DIFFRACTION6chain 'B' and (resid 1126 through 1391 )
7X-RAY DIFFRACTION7chain 'B' and (resid 1392 through 1551 )
8X-RAY DIFFRACTION8chain 'B' and (resid 1552 through 2037 )

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