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- PDB-7l4e: Crosslinked Crystal Structure of Type II Fatty Acid Synthase Keto... -

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Basic information

Entry
Database: PDB / ID: 7l4e
TitleCrosslinked Crystal Structure of Type II Fatty Acid Synthase Ketosynthase, FabF, and C16:1-crypto Acyl Carrier Protein, AcpP
Components
  • 3-oxoacyl-[acyl-carrier-protein] synthase 2
  • Acyl carrier protein
KeywordsTRANSFERASE / Thiolase / ketosynthase / KS / AcpP / ACP
Function / homology
Function and homology information


fatty acid elongation, saturated fatty acid / monounsaturated fatty acid biosynthetic process / beta-ketoacyl-[acyl-carrier-protein] synthase II / lipid A biosynthetic process / lipid biosynthetic process / acyl binding / acyl carrier activity / phosphopantetheine binding / 3-oxoacyl-[acyl-carrier-protein] synthase activity / response to cold ...fatty acid elongation, saturated fatty acid / monounsaturated fatty acid biosynthetic process / beta-ketoacyl-[acyl-carrier-protein] synthase II / lipid A biosynthetic process / lipid biosynthetic process / acyl binding / acyl carrier activity / phosphopantetheine binding / 3-oxoacyl-[acyl-carrier-protein] synthase activity / response to cold / fatty acid biosynthetic process / response to xenobiotic stimulus / lipid binding / protein homodimerization activity / membrane / cytoplasm / cytosol
Similarity search - Function
3-oxoacyl-[acyl-carrier-protein] synthase 2 / Beta-ketoacyl synthase / ACP-like / Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A / 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 ...3-oxoacyl-[acyl-carrier-protein] synthase 2 / Beta-ketoacyl synthase / ACP-like / Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A / 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 / Acyl carrier protein (ACP) / Thiolase-like / Phosphopantetheine attachment site / Phosphopantetheine attachment site. / Phosphopantetheine attachment site / ACP-like superfamily / Carrier protein (CP) domain profile. / Phosphopantetheine binding ACP domain / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-MU4 / Acyl carrier protein / 3-oxoacyl-[acyl-carrier-protein] synthase 2
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2 Å
AuthorsMindrebo, J.T. / Chen, A. / Kim, W.E. / Burkart, M.D. / Noel, J.P.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)095970-09 United States
CitationJournal: Acs Catalysis / Year: 2021
Title: Structure and Mechanistic Analyses of the Gating Mechanism of Elongating Ketosynthases
Authors: Mindrebo, J.T. / Chen, A. / Kim, W.E. / Re, R.N. / Davis, T.D. / Noel, J.P. / Burkart, M.D.
History
DepositionDec 18, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 6, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 3-oxoacyl-[acyl-carrier-protein] synthase 2
B: Acyl carrier protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,4395
Polymers51,7352
Non-polymers7043
Water5,116284
1
A: 3-oxoacyl-[acyl-carrier-protein] synthase 2
B: Acyl carrier protein
hetero molecules

A: 3-oxoacyl-[acyl-carrier-protein] synthase 2
B: Acyl carrier protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,87810
Polymers103,4704
Non-polymers1,4086
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_554-y,-x,-z-1/21
Buried area10970 Å2
ΔGint-50 kcal/mol
Surface area32280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.950, 86.950, 114.480
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-613-

HOH

21A-784-

HOH

31A-837-

HOH

41A-852-

HOH

51A-857-

HOH

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Components

#1: Protein 3-oxoacyl-[acyl-carrier-protein] synthase 2 / 3-oxoacyl-[acyl-carrier-protein] synthase II / Beta-ketoacyl-ACP synthase II / KAS II


Mass: 43089.629 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12 / Gene: fabF, fabJ, b1095, JW1081 / Plasmid: pET28 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P0AAI5, beta-ketoacyl-[acyl-carrier-protein] synthase II
#2: Protein Acyl carrier protein / ACP / Cytosolic-activating factor / CAF / Fatty acid synthase acyl carrier protein


Mass: 8645.460 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12 / Gene: acpP, b1094, JW1080 / Plasmid: pET28 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P0A6A8
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-MU4 / N-[2-(hexadecanoylamino)ethyl]-N~3~-[(2R)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alaninamide


Mass: 579.707 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H54N3O8P / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 284 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.09 Å3/Da / Density % sol: 41.18 % / Mosaicity: 0.63 °
Crystal growTemperature: 281 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 30 % PEG 8K, 0.1 M sodium cacodylate pH 6.5, and 0.3 M sodium acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 10, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→86.95 Å / Num. obs: 30391 / % possible obs: 100 % / Redundancy: 20.5 % / Biso Wilson estimate: 24.31 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.438 / Rpim(I) all: 0.099 / Rrim(I) all: 0.449 / Net I/σ(I): 8.7 / Num. measured all: 622935 / Scaling rejects: 778
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2-2.0518.84.3964122321980.5491.0374.5191.499.9
8.94-86.95190.11680234230.9940.0260.11923.4100

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
PHENIX1.13_2998refinement
MOSFLMdata reduction
Aimless0.7.4data scaling
PHASERphasing
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6OKG

6okg


Resolution: 2→69.242 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 19.44 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2069 1992 6.57 %
Rwork0.1671 28325 -
obs0.1697 30317 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 114.1 Å2 / Biso mean: 32.33 Å2 / Biso min: 11.26 Å2
Refinement stepCycle: final / Resolution: 2→69.242 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3602 0 46 284 3932
Biso mean--51.18 38.92 -
Num. residues----488
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
2-2.050.34041390.28061970
2.05-2.10550.33121400.25171973
2.1055-2.16740.24841390.21262002
2.1674-2.23740.25341400.20161990
2.2374-2.31730.26141400.1991983
2.3173-2.41010.25981420.18482002
2.4101-2.51980.23211400.17541996
2.5198-2.65270.26071420.1692005
2.6527-2.81890.20461430.17042021
2.8189-3.03650.19191400.16632015
3.0365-3.34210.18781450.15552040
3.3421-3.82570.16591430.14192047
3.8257-4.81980.13681460.12492084
4.8198-69.2420.21641530.15872197
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)
16.9923-0.7509-0.96321.4481-0.27951.03020.1215-0.2728-0.24130.1038-0.12060.00920.12620.13850.03890.2230.0167-0.03350.11640.01720.10560.2712-14.7567-9.1532
23.67841.01180.55830.7010.38711.146-0.0188-0.32220.46920.2392-0.11310.1704-0.0263-0.08730.13460.22810.01310.01570.1645-0.05370.2209-12.03832.2355-11.7365
32.7593-1.1534-1.49332.9659-0.56481.76710.0527-0.1873-0.00350.1412-0.0166-0.02880.08290.3524-0.04130.1744-0.0016-0.02860.1829-0.04830.10548.7082-3.5359-12.482
46.4284-1.52181.1666.5574-2.80114.538-0.0494-0.15520.01790.2590.06780.1617-0.2596-0.1786-0.0350.17910.01530.0040.1228-0.03460.1351-5.978615.262-24.3004
51.4581-0.04440.49690.43080.08761.44960.07350.00530.0505-0.0177-0.00640.01710.12780.1233-0.06290.15910.0332-0.00490.151-0.00180.13614.5965-5.3441-21.2116
61.4140.02560.14560.85460.21540.97510.0643-0.0409-0.1450.1321-0.01590.0720.26780.006-0.05430.2378-0.0085-0.01430.10460.02110.1334-5.1714-14.994-17.5541
74.4117-3.14555.35274.9802-4.19387.92060.12830.39720.0887-0.2047-0.0050.45390.4351-0.1208-0.24870.3660.0105-0.01450.2036-0.00940.296-4.5065-21.5934-34.08
81.5837-2.10750.1933.6791-0.58750.99840.16060.0703-0.4228-0.1281-0.03630.27240.7133-0.1604-0.05330.4671-0.0291-0.04750.1605-0.02740.291-7.9732-27.6681-24.7141
93.2436-0.7995-0.10722.4613-0.43950.98970.1087-0.0433-0.3915-0.0536-0.08510.09790.5445-0.1528-0.03470.3886-0.0544-0.0250.15940.02120.2047-10.0961-23.3717-14.7955
103.7561-1.76341.55857.3282-5.1059.0472-0.0454-0.1625-0.07950.18730.1420.07370.089-0.0575-0.13970.2640.0565-0.01160.12-0.04460.1472-0.0223-21.6806-22.2631
113.361-4.17482.61168.923-0.2287.59230.10160.53730.4957-0.75210.11940.1562-1.1077-0.6977-0.33520.41310.042-0.05470.44270.09950.2725-28.63473.823-51.8853
125.08824.50332.30264.86170.88644.91130.53481.0243-0.3624-0.73240.6533-0.42780.81230.0899-1.13430.3542-0.0857-0.0160.5875-0.08060.3229-23.2887-2.3352-58.9228
136.94470.46912.21137.17331.67712.42590.29340.4658-1.004-0.15780.27530.48011.3243-0.6391-0.47930.4766-0.1356-0.0780.39540.00640.3873-26.9546-9.0879-50.6298
143.0803-4.92880.16298.62290.23487.4109-0.31730.18860.57110.17450.3452-0.5481-0.7694-0.71330.08590.2680.059-0.0290.25420.01730.3398-25.49051.4337-41.4287
154.5724-1.5609-1.3978.05365.30563.7236-0.2001-0.67760.11561.2241-0.05250.77661.0341-1.23410.27170.5566-0.12240.03720.7560.06330.4116-33.4516-2.2393-38.1224
166.07642.93411.07443.0596-2.12644.4509-0.1255-1.39710.42860.22280.30191.1151-0.4205-1.71260.07840.29040.0395-0.10651.30550.03740.5731-38.29151.49-45.7054
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 28 )A2 - 28
2X-RAY DIFFRACTION2chain 'A' and (resid 29 through 71 )A29 - 71
3X-RAY DIFFRACTION3chain 'A' and (resid 72 through 110 )A72 - 110
4X-RAY DIFFRACTION4chain 'A' and (resid 111 through 138 )A111 - 138
5X-RAY DIFFRACTION5chain 'A' and (resid 139 through 204 )A139 - 204
6X-RAY DIFFRACTION6chain 'A' and (resid 205 through 264 )A205 - 264
7X-RAY DIFFRACTION7chain 'A' and (resid 265 through 290 )A265 - 290
8X-RAY DIFFRACTION8chain 'A' and (resid 291 through 327 )A291 - 327
9X-RAY DIFFRACTION9chain 'A' and (resid 328 through 391 )A328 - 391
10X-RAY DIFFRACTION10chain 'A' and (resid 392 through 412 )A392 - 412
11X-RAY DIFFRACTION11chain 'B' and (resid 1 through 15 )B1 - 15
12X-RAY DIFFRACTION12chain 'B' and (resid 16 through 21 )B16 - 21
13X-RAY DIFFRACTION13chain 'B' and (resid 22 through 35 )B22 - 35
14X-RAY DIFFRACTION14chain 'B' and (resid 36 through 50 )B36 - 50
15X-RAY DIFFRACTION15chain 'B' and (resid 51 through 64 )B51 - 64
16X-RAY DIFFRACTION16chain 'B' and (resid 65 through 77 )B65 - 77

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