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

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Basic information

Entry
Database: PDB / ID: 6olt
TitleCrosslinked Crystal Structure of Type II Fatty Acid Synthase Ketosynthase, FabF, and C12-crypto Acyl Carrier Protein, AcpP
Components
  • 3-oxoacyl-[acyl-carrier-protein] synthase 2
  • Acyl carrier protein
KeywordsTRANSFERASE / ketosynthase / KS / AcpP / beta-ketoacyl-Acyl carrier protein synthase / beta-ketoacyl-ACP synthase / acyl carrier protein / TRANSFERASE-TRANSPORT PROTEIN complex
Function / homology
Function and homology information


fatty acid elongation, saturated fatty acid / monounsaturated fatty acid biosynthetic process / beta-ketoacyl-[acyl-carrier-protein] synthase II / acyl binding / lipid biosynthetic process / lipid A biosynthetic process / 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 / acyl binding / lipid biosynthetic process / lipid A biosynthetic process / 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 / 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 / Phosphopantetheine attachment site. / Thiolase-like / 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 2
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.35 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 17, 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.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)52,2593
Polymers51,7352
Non-polymers5241
Water1,65792
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)104,5176
Polymers103,4704
Non-polymers1,0472
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_554-y,-x,-z-1/21
Buried area9270 Å2
ΔGint-57 kcal/mol
Surface area33280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.450, 86.450, 115.160
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-601-

HOH

21A-631-

HOH

31A-686-

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-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.: 1 / Source method: obtained synthetically / Formula: C23H46N3O8P / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 92 / 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: 2.08 Å3/Da / Density % sol: 40.87 %
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
Temp details: 279

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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: 2.35→86.45 Å / Num. obs: 18833 / % possible obs: 99.9 % / Redundancy: 15.3 % / Biso Wilson estimate: 40.96 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.331 / Rpim(I) all: 0.086 / Rrim(I) all: 0.342 / Net I/σ(I): 9.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
2.35-2.4315.94.09817980.4481.0494.23299.8
9.1-86.4512.90.044050.9990.0120.042100

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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_EXTRACT3.25data 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: 2.35→69.137 Å / SU ML: 0.32 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 25.84
RfactorNum. reflection% reflection
Rfree0.2389 1075 5.73 %
Rwork0.2006 --
obs0.2029 18770 99.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 162.33 Å2 / Biso mean: 58.9403 Å2 / Biso min: 21.73 Å2
Refinement stepCycle: final / Resolution: 2.35→69.137 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3608 0 48 92 3748
Biso mean--58.36 46.56 -
Num. residues----489
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 8 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.35-2.4570.31611220.31321702292
2.457-2.58650.39271270.296321682295
2.5865-2.74860.35071350.280321562291
2.7486-2.96080.30641240.259421882312
2.9608-3.25880.22861400.223421832323
3.2588-3.73030.25151380.187922192357
3.7303-4.69970.18891410.142422362377
4.6997-69.16670.19091480.173323752523
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)
12.62610.11160.43051.11880.19692.6321-0.0168-0.2523-0.01750.37260.02690.18440.6612-0.11080.04260.4837-0.01090.030.3153-0.00760.2754-6.8894-3.934-10.865
21.4525-0.69270.53792.5445-0.10813.84310.02230.02920.13560.2505-0.0838-0.11440.1150.3950.09670.20250.0321-0.00310.2843-0.0250.30632.02144.9248-17.9955
32.5159-0.10890.19571.09280.38113.20220.216-0.0982-0.39330.2311-0.01570.00540.83060.2048-0.13970.47540.1041-0.05280.20.01570.3322-1.4242-8.763-19.7487
40.7457-0.6949-0.81322.8272-1.12492.47850.2840.2082-0.2963-0.1132-0.00840.40521.55360.2246-0.36040.80270.1619-0.12150.3303-0.04230.5148-2.3493-19.7988-30.1943
51.8055-1.31390.09061.3985-0.37790.24460.26780.2861-0.60640.1417-0.1570.29921.5188-0.1726-0.14871.1589-0.0446-0.08660.30.01080.5682-7.1065-23.2933-20.3408
62.3708-0.7748-2.46942.575-0.25233.1543-0.1184-0.048-0.56440.19340.13840.26181.5758-0.394-0.02121.1539-0.1148-0.13070.39080.00470.5354-8.4229-24.3416-18.9279
78.99-3.3173-3.70328.13094.70794.85860.71271.16480.7221-1.0966-0.14240.0281-1.4636-1.302-0.52020.81490.0623-0.04140.89140.22320.4265-27.25362.2842-53.7148
88.3878-4.06730.42195.7108-3.08144.9279-0.08791.8901-1.7099-0.54880.36230.80831.9654-0.8831-0.44021.0405-0.3615-0.11920.8605-0.13010.6325-28.2831-8.9729-52.844
92.46651.82491.71147.133.98912.91740.12150.07310.2182-0.28840.4236-0.5431-0.5025-0.6805-0.6650.54380.0249-0.04610.48650.00160.554-24.7172-1.1909-43.2518
106.28161.9067-2.41034.6736-4.75314.9044-0.0893-0.1478-0.18462.3207-1.2844-0.1133-1.6585-0.24361.56680.7537-0.11870.00961.1261-0.00690.4669-33.47334.8701-36.5382
116.32191.07155.45688.5455-0.51564.96560.2467-1.5948-0.25531.51530.09620.64230.345-1.5215-0.37320.996-0.49510.04951.44640.22650.857-33.1314-6.7035-38.7933
123.8442.22181.61381.8815-1.33259.28380.4981-2.49460.19210.5992-0.25750.7064-0.4596-2.8894-0.02370.6921-0.0585-0.1242.3557-0.10470.8239-37.80370.9372-45.704
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 71 )A1 - 71
2X-RAY DIFFRACTION2chain 'A' and (resid 72 through 138 )A72 - 138
3X-RAY DIFFRACTION3chain 'A' and (resid 139 through 249 )A139 - 249
4X-RAY DIFFRACTION4chain 'A' and (resid 250 through 290 )A250 - 290
5X-RAY DIFFRACTION5chain 'A' and (resid 291 through 359 )A291 - 359
6X-RAY DIFFRACTION6chain 'A' and (resid 360 through 412 )A360 - 412
7X-RAY DIFFRACTION7chain 'B' and (resid 1 through 20 )B1 - 20
8X-RAY DIFFRACTION8chain 'B' and (resid 21 through 30 )B21 - 30
9X-RAY DIFFRACTION9chain 'B' and (resid 31 through 50 )B31 - 50
10X-RAY DIFFRACTION10chain 'B' and (resid 51 through 55 )B51 - 55
11X-RAY DIFFRACTION11chain 'B' and (resid 56 through 64 )B56 - 64
12X-RAY DIFFRACTION12chain 'B' and (resid 65 through 77 )B65 - 77

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