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- PDB-7sz9: Crosslinked Crystal Structure of Type II Fatty Acid Synthase Keto... -

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Basic information

Entry
Database: PDB / ID: 7sz9
TitleCrosslinked Crystal Structure of Type II Fatty Acid Synthase Ketosynthase, FabB, and C16:1-crypto Acyl Carrier Protein, AcpP
Components
  • 3-oxoacyl-[acyl-carrier-protein] synthase 1
  • Acyl carrier protein
KeywordsTRANSFERASE / ketosynthase / crosslink / FabB / ACP / KASI
Function / homology
Function and homology information


monounsaturated fatty acid biosynthetic process / beta-ketoacyl-[acyl-carrier-protein] synthase I / lipid A biosynthetic process / acyl binding / acyl carrier activity / 3-oxoacyl-[acyl-carrier-protein] synthase activity / fatty acid biosynthetic process / membrane / cytosol
Similarity search - Function
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 / 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-DJ5 / Acyl carrier protein / 3-oxoacyl-[acyl-carrier-protein] synthase 1
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsMindrebo, J.T. / Chen, A. / Noel, J.P. / Burkart, M.D.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM097907 United States
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2022
Title: Mechanism-based cross-linking probes capture the Escherichia coli ketosynthase FabB in conformationally distinct catalytic states.
Authors: Chen, A. / Mindrebo, J.T. / Davis, T.D. / Kim, W.E. / Katsuyama, Y. / Jiang, Z. / Ohnishi, Y. / Noel, J.P. / Burkart, M.D.
History
DepositionNov 26, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 23, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Nov 13, 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 1
B: 3-oxoacyl-[acyl-carrier-protein] synthase 1
C: Acyl carrier protein
D: Acyl carrier protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,4228
Polymers102,2214
Non-polymers1,2014
Water2,972165
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10440 Å2
ΔGint-60 kcal/mol
Surface area31890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.450, 103.580, 79.280
Angle α, β, γ (deg.)90.000, 108.280, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 42596.129 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12 / Gene: fabB, fabC, b2323, JW2320 / Plasmid: pET28 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: P0A953, beta-ketoacyl-[acyl-carrier-protein] synthase I
#2: Protein Acyl carrier protein / ACP


Mass: 8514.264 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: acpP, ECS88_1108 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: B7MJ81
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-DJ5 / N~3~-{(2R)-4-[(dihydroxyphosphanyl)oxy]-2-hydroxy-3,3-dimethylbutanoyl}-N-(2-{[(9Z)-hexadec-9-enoyl]amino}ethyl)-beta-alaninamide


Mass: 577.691 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H52N3O8P
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 165 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.27 Å3/Da / Density % sol: 45.82 %
Crystal growTemperature: 281 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 20% PEG 8000, 0.3 M sodium acetate, 0.1 M sodium cacodylate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 6, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→75.28 Å / Num. obs: 38093 / % possible obs: 82.1 % / Redundancy: 2.1 % / Biso Wilson estimate: 32.53 Å2 / CC1/2: 0.945 / R split: 0.176 / Rmerge(I) obs: 0.205 / Rpim(I) all: 0.117 / Rrim(I) all: 0.238 / Χ2: 1.15 / Net I/σ(I): 3.7
Reflection shell
Resolution (Å)Num. unique obsCC1/2Diffraction-ID% possible all
2.2-2.2414120.576153.9
11.22-60.93720.986198.3

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Processing

Software
NameVersionClassification
Aimlessdata scaling
PHENIX1.19.2_4158refinement
PDB_EXTRACT3.27data extraction
iMOSFLMdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6okc

6okc


Resolution: 2.2→54.02 Å / SU ML: 0.3 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 29.31 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2554 1808 4.77 %
Rwork0.2083 36100 -
obs0.2105 37908 81.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 188.1 Å2 / Biso mean: 56.7525 Å2 / Biso min: 16.47 Å2
Refinement stepCycle: final / Resolution: 2.2→54.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7011 0 75 165 7251
Biso mean--77.5 45.8 -
Num. residues----957
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.2-2.260.3547980.31161820191854
2.26-2.330.3393950.30891786188153
2.33-2.40.33851190.29181836195555
2.4-2.490.34681430.30852666280980
2.49-2.590.30451370.29322724286180
2.59-2.70.33581580.27062716287481
2.7-2.850.34721200.26932733285380
2.85-3.030.26741490.25342740288982
3.03-3.260.29581710.22663368353999
3.26-3.590.2951530.20463407356099
3.59-4.10.20211370.168734103547100
4.11-5.170.16861510.151634373588100
5.17-54.020.21051770.174134573634100
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)
11.98950.45840.57341.9995-0.08661.00940.2442-0.0989-0.39170.19850.0645-0.25710.20910.1978-0.2680.20180.02-0.1160.4371-0.07920.362123.419221.414328.0106
21.85930.39390.56672.18730.38781.39270.17280.1473-0.3547-0.14970.06650.00880.16940.2363-0.23820.15710.0361-0.05590.4563-0.0360.298820.460323.293717.838
32.1328-1.3441-0.53651.83580.11152.44290.07180.9398-0.3719-0.41310.1495-0.10530.18320.2296-0.14190.2872-0.00740.04870.7144-0.17980.373223.955224.1744.004
41.6050.1910.23991.68570.23491.28870.0774-0.0378-0.10850.159-0.10820.04940.12860.02660.04120.1439-0.0374-0.00380.31020.00070.1967-2.985927.678124.4552
54.95141.110.34892.03042.42943.1397-0.1153-0.76980.23060.13140.0455-0.12070.03220.38430.06020.1811-0.02430.05540.3797-0.03730.26384.226245.788630.0542
61.87670.3924-1.11962.58190.25612.50670.0836-0.78660.35470.4737-0.0811-0.0695-0.14770.01070.01380.2274-0.02540.01250.5107-0.10090.299-4.055345.157135.3655
77.7569-2.47520.48197.6174-3.96392.23620.152-2.0510.38161.6729-0.4472-1.2549-0.71951.29910.28771.0909-0.1444-0.38221.251-0.03220.851825.957823.921357.2489
83.93791.17554.01084.70193.2925.09710.7756-0.681-1.07391.3748-0.041-0.32130.67660.367-0.62420.9406-0.1153-0.08510.78340.12440.406717.775221.296652.3378
94.16410.151.91093.37735.28218.9350.2712-1.8925-0.35530.0174-0.56060.42171.19430.05040.20361.374-0.21860.31011.05920.13641.095511.408719.762460.1782
101.96210.7661-0.56680.86680.3480.73310.24760.05810.20320.1556-0.05490.1536-0.003-0.4109-0.21520.79710.01230.00060.47570.0730.358518.357617.061465.7248
116.06153.8801-4.0458.2697-5.50944.2625-0.117-0.08740.05481.0192-0.05490.76550.2109-1.96750.1420.6077-0.02530.05511.0975-0.22410.2884-13.1405-3.136111.803
122.6661-0.9308-2.49718.08572.8082.8214-0.46250.35640.46340.14030.25231.2241-0.5231-1.48350.21660.5220.2143-0.00871.6112-0.35460.8111-15.08271.1813.3544
134.6694.62083.85544.96884.10213.3905-0.11691.5667-0.3424-1.73120.5264-0.8501-0.8176-0.0127-0.36560.6373-0.02550.04970.5416-0.18030.4121-4.86323.73561.4111
146.32326.6898-5.43847.1067-5.84374.940.8155-1.1202-0.36741.5864-1.3189-0.7624-1.1178-0.02820.44860.7272-0.0324-0.15540.55920.01840.5778-1.72870.249414.4798
159.51881.29122.10575.8216-1.6021.3861-0.1809-0.9701-1.2290.8999-0.239-0.3652.03010.25620.34321.00390.06330.07540.5999-0.05160.373-1.6733-9.754517.5145
168.4078-0.3206-3.15747.182-4.84617.4862-0.4087-0.4409-0.94480.1638-0.1991-1.78971.48992.07240.52180.63180.32860.04530.6982-0.22560.92993.1022-6.49596.3364
177.04412.76832.76275.7044-2.55463.9540.3467-0.2266-1.48590.17360.2218-0.62.4933-0.3772-0.4891.01750.0370.09340.4462-0.03640.4199-6.2976-11.58488.1782
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 0 through 147 )A0 - 147
2X-RAY DIFFRACTION2chain 'A' and (resid 148 through 248 )A148 - 248
3X-RAY DIFFRACTION3chain 'A' and (resid 249 through 405 )A249 - 405
4X-RAY DIFFRACTION4chain 'B' and (resid 0 through 248 )B0 - 248
5X-RAY DIFFRACTION5chain 'B' and (resid 249 through 304 )B249 - 304
6X-RAY DIFFRACTION6chain 'B' and (resid 305 through 404 )B305 - 404
7X-RAY DIFFRACTION7chain 'C' and (resid 5 through 30 )C5 - 30
8X-RAY DIFFRACTION8chain 'C' and (resid 31 through 49 )C31 - 49
9X-RAY DIFFRACTION9chain 'C' and (resid 50 through 64 )C50 - 64
10X-RAY DIFFRACTION10chain 'C' and (resid 65 through 75 )C65 - 75
11X-RAY DIFFRACTION11chain 'D' and (resid 1 through 15 )D1 - 15
12X-RAY DIFFRACTION12chain 'D' and (resid 16 through 25 )D16 - 25
13X-RAY DIFFRACTION13chain 'D' and (resid 26 through 35 )D26 - 35
14X-RAY DIFFRACTION14chain 'D' and (resid 36 through 49 )D36 - 49
15X-RAY DIFFRACTION15chain 'D' and (resid 50 through 55 )D50 - 55
16X-RAY DIFFRACTION16chain 'D' and (resid 56 through 64 )D56 - 64
17X-RAY DIFFRACTION17chain 'D' and (resid 65 through 75 )D65 - 75

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