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- PDB-6okf: Crosslinked Crystal Structure of Type II Fatty Acid Synthase Keto... -

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Basic information

Entry
Database: PDB / ID: 6okf
TitleCrosslinked Crystal Structure of Type II Fatty Acid Synthase Ketosynthase, FabB, and C16-crypto Acyl Carrier Protein, AcpP
Components
  • 3-oxoacyl-[acyl-carrier-protein] synthase 1
  • Acyl carrier protein
KeywordsTRANSFERASE/TRANSPORT PROTEIN / Thiolase fold / fatty acid synthase / ketosynthase / beta-Ketoacyl-ACP Synthase / KS / AcpP / TRANSFERASE-TRANSPORT PROTEIN complex
Function / homology
Function and homology information


monounsaturated fatty acid biosynthetic process / beta-ketoacyl-[acyl-carrier-protein] synthase I / lipid A biosynthetic process / lipid biosynthetic process / acyl binding / phosphopantetheine binding / acyl carrier activity / 3-oxoacyl-[acyl-carrier-protein] synthase activity / fatty acid biosynthetic process / response to xenobiotic stimulus ...monounsaturated fatty acid biosynthetic process / beta-ketoacyl-[acyl-carrier-protein] synthase I / lipid A biosynthetic process / lipid biosynthetic process / acyl binding / phosphopantetheine binding / acyl carrier activity / 3-oxoacyl-[acyl-carrier-protein] synthase activity / fatty acid biosynthetic process / response to xenobiotic stimulus / lipid binding / cytosol / cytoplasm
Similarity search - Function
Beta-ketoacyl synthase / Thiolase/Chalcone synthase / Peroxisomal Thiolase; Chain A, domain 1 / Ketosynthase family 3 (KS3) domain profile. / Beta-ketoacyl synthase / Beta-ketoacyl synthase, active site / Ketosynthase family 3 (KS3) active site signature. / Polyketide synthase, beta-ketoacyl synthase domain / Beta-ketoacyl synthase, N-terminal / Beta-ketoacyl synthase, C-terminal ...Beta-ketoacyl synthase / Thiolase/Chalcone synthase / Peroxisomal Thiolase; Chain A, domain 1 / Ketosynthase family 3 (KS3) domain profile. / Beta-ketoacyl synthase / Beta-ketoacyl synthase, active site / Ketosynthase family 3 (KS3) active site signature. / Polyketide synthase, beta-ketoacyl synthase domain / Beta-ketoacyl synthase, N-terminal / Beta-ketoacyl synthase, C-terminal / Beta-ketoacyl synthase, N-terminal domain / Beta-ketoacyl synthase, C-terminal domain / Acyl carrier protein (ACP) / Phosphopantetheine attachment site / Thiolase-like / Phosphopantetheine attachment site. / Phosphopantetheine attachment site / ACP-like superfamily / Carrier protein (CP) domain profile. / Phosphopantetheine binding ACP domain / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-MRJ / Acyl carrier protein / 3-oxoacyl-[acyl-carrier-protein] synthase 1
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.5 Å
AuthorsMindrebo, J.T. / Kim, W.E. / Bartholow, T.G. / Chen, A. / Davis, T.D. / La Clair, J. / Burkart, M.D. / Noel, J.P.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)5R01GM095970-06 United States
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: Nat Commun / Year: 2020
Title: Gating mechanism of elongating beta-ketoacyl-ACP synthases.
Authors: Mindrebo, J.T. / Patel, A. / Kim, W.E. / Davis, T.D. / Chen, A. / Bartholow, T.G. / La Clair, J.J. / McCammon, J.A. / Noel, J.P. / Burkart, M.D.
History
DepositionApr 12, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 22, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id

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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)103,6978
Polymers102,6034
Non-polymers1,0934
Water1,928107
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10460 Å2
ΔGint-54 kcal/mol
Surface area31280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.939, 100.781, 79.260
Angle α, β, γ (deg.)90.000, 108.640, 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: 42656.203 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 / Cytosolic-activating factor / CAF / Fatty acid synthase acyl carrier protein


Mass: 8645.460 Da / Num. of mol.: 2
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) / Strain (production host): BL21(DE3) / References: UniProt: P0A6A8
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: Na
#4: Chemical ChemComp-MRJ / N-[2-(dodecanoylamino)ethyl]-N~3~-[(2R)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alaninamide


Mass: 523.600 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C23H46N3O8P / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 107 / 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: 2.17 Å3/Da / Density % sol: 43.42 % / Mosaicity: 0.5 °
Crystal growTemperature: 281 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 26% 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: 5.0.2 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 10, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→75.102 Å / Num. obs: 30131 / % possible obs: 99 % / Redundancy: 6.2 % / Biso Wilson estimate: 45.42 Å2 / CC1/2: 0.993 / Rmerge(I) obs: 0.14 / Rpim(I) all: 0.061 / Rrim(I) all: 0.153 / Net I/σ(I): 7.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
2.5-2.66.40.83233840.910.3530.90698.6
9.01-60.226.20.0676810.9960.0290.07399.2

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
PHENIX1.13_2998refinement
MOSFLMdata reduction
Aimless0.5.32data scaling
PHASERphasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1G5X (FabB), 2FAC (AcpP)

1g5x

2fac


Resolution: 2.5→75.102 Å / SU ML: 0.31 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 23.85
RfactorNum. reflection% reflection
Rfree0.2184 1642 5.46 %
Rwork0.1764 --
obs0.1786 30073 98.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 192.04 Å2 / Biso mean: 65.1611 Å2 / Biso min: 25.16 Å2
Refinement stepCycle: final / Resolution: 2.5→75.102 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7106 0 70 107 7283
Biso mean--72.16 49.75 -
Num. residues----960
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.5-2.57360.29121220.26322379250198
2.5736-2.65660.291350.23732343247898
2.6566-2.75160.28551310.23552326245798
2.7516-2.86180.30041350.22092346248199
2.8618-2.9920.2691390.22122347248698
2.992-3.14980.29461450.22232358250398
3.1498-3.34710.24021340.19112375250999
3.3471-3.60550.20291610.17882353251499
3.6055-3.96840.21291530.162359251299
3.9684-4.54250.16741250.14742402252799
4.5425-5.72280.20421120.15182411252399
5.7228-75.1360.17561500.14682432258299
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)
13.00190.20691.29671.65620.01181.78820.20510.175-0.1275-0.1626-0.1436-0.25680.18250.2457-0.08440.22540.0440.01160.4391-0.01980.406760.2281-9.564586.3197
23.12991.1662.40777.15634.49454.59590.2502-0.2342-0.55270.21580.06820.06580.37040.0501-0.27320.2732-0.0319-0.02110.52670.0820.37948.8725-17.850494.2665
33.1337-0.28970.91661.5417-0.29692.29320.0847-0.04370.0347-0.0550.03150.05970.07270.0402-0.09130.1752-0.0127-0.00490.3940.00790.353850.4029-4.512287.5684
44.2118-0.85430.17072.658-0.56772.2421-0.09490.7080.5888-0.3553-0.05590.0728-0.1347-0.00640.12110.2849-0.05030.01880.46960.10450.510951.81848.277777.5478
53.0888-0.61110.38171.1924-0.95290.76110.3411-0.778-1.0703-0.26980.19180.84060.522-0.60930.00750.2692-0.232-0.24950.94610.29860.76621.9001-21.095993.7693
63.8146-0.6150.71435.75920.70451.970.1183-0.0304-0.1518-0.33310.0430.52670.1725-0.2863-0.12630.2282-0.0394-0.02820.48240.14020.363324.695-7.480881.3075
72.6205-1.2831-0.27793.7157-3.10983.44180.18750.9297-0.3417-0.94690.04760.16920.5419-0.8058-0.33030.53550.0491-0.07030.6057-0.10280.615241.5437-23.305872.3683
81.6934-0.02740.18371.21380.111.6910.0929-0.35190.02440.04530.11-0.12760.0725-0.1603-0.17920.21880.0064-0.01060.55350.0120.407932.9109-4.621888.3514
93.85921.2227-1.1273.11820.28223.85250.1906-1.1187-1.2809-0.07020.32960.56520.7246-0.0135-0.30720.4581-0.1419-0.20220.74390.40370.992531.1433-30.427999.5356
101.61620.68570.9821.6418-0.75882.2515-0.026-0.8762-0.16550.39770.03940.1099-0.1003-0.38980.00240.2962-0.00090.08751.0680.0540.481528.92-5.0326104.7051
113.08182.11360.04182.11990.48462.09590.2795-1.1237-0.52750.64350.17240.20130.2987-0.4535-0.33130.4584-0.0290.00131.19710.34150.615824.7228-15.1142108.823
129.2047-4.6356-3.95947.92543.07515.6726-0.1050.6170.6649-1.10140.3171-1.15610.52771.1721-0.21580.7763-0.08640.01861.24490.19670.578964.4494-37.6042102.8336
136.686-3.0232-0.80286.26032.18165.19290.1885-0.3433-1.1287-0.86290.1481.21140.17110.2978-0.10870.7114-0.0685-0.20180.6060.33160.906854.3481-37.2139102.9368
143.08540.83624.66146.94991.90317.1040.7284-0.5757-1.562-1.46720.17942.3631.6365-1.2382-0.66240.9583-0.1721-0.32311.00960.4241.361951.9656-45.8855104.9615
158.7358-5.4174-3.88237.3570.90232.2906-0.54011.3391-1.0942-0.4676-0.98811.46570.1624-2.73631.40470.8227-0.1125-0.00591.5874-0.22191.173426.3954-19.658152.749
166.6607-0.1078-4.80042.069-1.05364.0790.5311-0.10330.7402-0.9063-0.23051.84570.1954-1.4735-0.30971.01810.1423-0.2051.71010.18131.38720.0794-11.893955.2321
172.0286-0.8314-2.3658.2041-0.85437.821-0.20872.3354-0.0239-2.0791-0.14671.1809-1.5860.30650.40431.00840.125-0.13511.34830.1340.71129.4247-6.702253.9355
189.15132.2515-0.04632.02111.28922.0296-0.40420.1198-1.7058-0.82350.0572-0.48220.5791-0.65180.27470.937-0.04770.15040.8645-0.11770.837136.8795-20.131958.4153
194.72760.07654.32735.309-2.28745.02540.21292.16310.076-0.36080.43950.10170.23560.8652-0.44091.1950.10480.07641.30150.04980.866838.7996-16.710248.8368
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 85 )A2 - 85
2X-RAY DIFFRACTION2chain 'A' and (resid 86 through 128 )A86 - 128
3X-RAY DIFFRACTION3chain 'A' and (resid 129 through 264 )A129 - 264
4X-RAY DIFFRACTION4chain 'A' and (resid 265 through 404 )A265 - 404
5X-RAY DIFFRACTION5chain 'B' and (resid 2 through 52 )B2 - 52
6X-RAY DIFFRACTION6chain 'B' and (resid 53 through 109 )B53 - 109
7X-RAY DIFFRACTION7chain 'B' and (resid 110 through 132 )B110 - 132
8X-RAY DIFFRACTION8chain 'B' and (resid 133 through 194 )B133 - 194
9X-RAY DIFFRACTION9chain 'B' and (resid 195 through 233 )B195 - 233
10X-RAY DIFFRACTION10chain 'B' and (resid 234 through 302 )B234 - 302
11X-RAY DIFFRACTION11chain 'B' and (resid 303 through 404 )B303 - 404
12X-RAY DIFFRACTION12chain 'C' and (resid 1 through 21 )C1 - 21
13X-RAY DIFFRACTION13chain 'C' and (resid 22 through 55 )C22 - 55
14X-RAY DIFFRACTION14chain 'C' and (resid 56 through 77 )C56 - 77
15X-RAY DIFFRACTION15chain 'D' and (resid 1 through 15 )D1 - 15
16X-RAY DIFFRACTION16chain 'D' and (resid 16 through 21 )D16 - 21
17X-RAY DIFFRACTION17chain 'D' and (resid 22 through 35 )D22 - 35
18X-RAY DIFFRACTION18chain 'D' and (resid 36 through 55 )D36 - 55
19X-RAY DIFFRACTION19chain 'D' and (resid 56 through 77 )D56 - 77

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