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

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Basic information

Entry
Database: PDB / ID: 6okg
TitleCrosslinked Crystal Structure of Type II Fatty Acid Synthase Ketosynthase, FabF, and C16-crypto Acyl Carrier Protein, AcpP
Components
  • 3-oxoacyl-[acyl-carrier-protein] synthase 2
  • Acyl carrier protein
KeywordsTRANSFERASE / Thiolase / ketosynthase / KS / AcpP
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 / phosphopantetheine binding / acyl binding / 3-oxoacyl-[acyl-carrier-protein] synthase activity / acyl carrier 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 / phosphopantetheine binding / acyl binding / 3-oxoacyl-[acyl-carrier-protein] synthase activity / acyl carrier activity / response to cold / fatty acid biosynthetic process / response to xenobiotic stimulus / lipid binding / protein homodimerization activity / cytosol / cytoplasm
Similarity search - Function
3-oxoacyl-[acyl-carrier-protein] synthase 2 / 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 ...3-oxoacyl-[acyl-carrier-protein] synthase 2 / 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-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: 2.3 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.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _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 2
B: Acyl carrier protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,3384
Polymers51,7352
Non-polymers6032
Water3,369187
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)104,6768
Polymers103,4704
Non-polymers1,2054
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_554-y,-x,-z-1/21
Buried area10090 Å2
ΔGint-59 kcal/mol
Surface area32630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.890, 86.890, 113.729
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-604-

HOH

21A-735-

HOH

31A-761-

HOH

41A-770-

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) / Strain (production host): BL21(DE3)
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) / Strain (production host): BL21(DE3) / References: UniProt: P0A6A8
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#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 / Water


Mass: 18.015 Da / Num. of mol.: 187 / 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: 2.07 Å3/Da / Density % sol: 40.71 % / Description: Orange Rods
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: Oct 14, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→86.89 Å / Num. obs: 20047 / % possible obs: 100 % / Redundancy: 19.1 % / Biso Wilson estimate: 27.25 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.368 / Rpim(I) all: 0.085 / Rrim(I) all: 0.378 / Net I/σ(I): 9.2 / Num. measured all: 382501 / Scaling rejects: 2023
Reflection shell

Diffraction-ID: 1 / % possible all: 100

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all
2.3-2.3819.82.39919280.5970.5442.461
8.91-86.89170.0614250.9990.0150.063

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
Aimless0.7.4data scaling
PHASERphasing
PHENIX1.13_2998refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2GFW was used as the search model for FabF, 2FAC was used as the search model for AcpP

2gfw

2fac


Resolution: 2.3→69.045 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 22.37 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2283 997 5 %
Rwork0.1938 18956 -
obs0.1955 19953 99.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 135.73 Å2 / Biso mean: 31.8894 Å2 / Biso min: 14.12 Å2
Refinement stepCycle: final / Resolution: 2.3→69.045 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3602 0 77 187 3866
Biso mean--33.18 31.91 -
Num. residues----487
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 7 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.3001-2.42130.29431400.275726552795
2.4213-2.57310.25961390.239126442783
2.5731-2.77170.29331410.242626702811
2.7717-3.05070.32461410.220526762817
3.0507-3.49210.2221410.189326982839
3.4921-4.39960.17371430.156327212864
4.3996-69.07590.19361520.163328923044
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)
11.896-0.02090.17730.5925-0.20871.06040.0771-0.0469-0.17150.1451-0.06950.11340.1319-0.04130.02270.2396-0.00240.01840.1411-0.02550.1366-8.8825-9.225-11.6393
23.87142.40590.96911.49020.48511.01410.0339-0.50310.34240.2042-0.19630.2619-0.1223-0.01480.14750.27330.02370.02990.2228-0.07360.2678-4.69985.3442-8.8184
30.8785-0.68930.58221.6897-0.41542.1027-0.0229-0.09350.1290.12150.0039-0.0092-0.08-0.0327-0.00490.1272-0.01770.00880.1515-0.01920.18411.93774.7607-17.8517
40.54980.0970.04420.44110.19230.63750.00810.08320.02710.05070.00640.0360.10360.0047-0.03240.21530.0221-0.00390.17130.00680.1985-1.7804-6.8396-20.8416
51.72350.0354-0.02410.95850.01941.0840.06270.1285-0.2080.0109-0.03560.03720.2536-0.0319-0.03780.2641-0.0095-0.00650.1362-0.00030.1918-3.408-20.9355-21.3374
65.5366-1.81210.65312.11960.03772.23390.31020.0522-0.316-0.077-0.2339-0.00380.5492-0.3019-0.14180.3559-0.0677-0.02050.15940.05020.2997-13.8324-27.7417-14.4919
72.5940.6741-1.75424.3583-0.07762.12150.1163-0.23490.1342-0.0459-0.0252-0.10340.19660.03190.07380.20750.0053-0.020.1438-0.00380.20710.0483-21.7033-22.0372
82.1733-1.6643-1.32232.04491.59139.48190.39290.93470.9465-0.1388-0.3509-0.2156-1.3576-1.00260.01040.43650.06180.01520.48170.08570.3909-28.50283.8775-51.5203
98.89180.62933.9243.2833-0.9662.22140.24650.86460.0374-1.34060.60790.26230.8163-1.1366-0.70230.5049-0.0952-0.04170.77910.04210.3521-23.1027-2.6043-58.2074
105.6384-0.36592.04653.3639-0.11016.9833-0.21660.2409-0.0447-0.08320.49440.1576-0.2164-0.4393-0.2340.2341-0.028-0.00360.30710.06750.2616-26.029-3.3042-45.2918
114.3822.14640.98787.60383.26949.0086-0.1008-0.38930.15790.4903-0.20941.1101-0.3889-1.84640.21180.40740.00250.07050.92310.07110.4795-35.5289-0.1695-40.9942
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 48 )A2 - 48
2X-RAY DIFFRACTION2chain 'A' and (resid 49 through 71 )A49 - 71
3X-RAY DIFFRACTION3chain 'A' and (resid 72 through 138 )A72 - 138
4X-RAY DIFFRACTION4chain 'A' and (resid 139 through 222 )A139 - 222
5X-RAY DIFFRACTION5chain 'A' and (resid 223 through 359 )A223 - 359
6X-RAY DIFFRACTION6chain 'A' and (resid 360 through 391 )A360 - 391
7X-RAY DIFFRACTION7chain 'A' and (resid 392 through 412 )A392 - 412
8X-RAY DIFFRACTION8chain 'B' and (resid 1 through 15 )B1 - 15
9X-RAY DIFFRACTION9chain 'B' and (resid 16 through 21 )B16 - 21
10X-RAY DIFFRACTION10chain 'B' and (resid 22 through 50 )B22 - 50
11X-RAY DIFFRACTION11chain 'B' and (resid 51 through 77 )B51 - 77

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