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- PDB-6smo: AntDE:AntF (apo): type II PKS acyl-carrier protein in complex wit... -

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Basic information

Entry
Database: PDB / ID: 6smo
TitleAntDE:AntF (apo): type II PKS acyl-carrier protein in complex with its ketosynthase bound to the hexaketide
Components
  • Acyl carrier protein
  • Ketoacyl_synth_N domain-containing protein
  • PKS_KS domain-containing protein
KeywordsPROTEIN BINDING / Natural Product Biosynthesis / Polyketides / Minimal PKS System / Anthraquinone / Chain Elongation / Catalysis
Function / homology
Function and homology information


3-oxoacyl-[acyl-carrier-protein] synthase activity / fatty acid biosynthetic process
Similarity search - Function
Beta-ketoacyl synthase / Thiolase/Chalcone synthase / Peroxisomal Thiolase; Chain A, domain 1 / Beta-ketoacyl synthase / 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 ...Beta-ketoacyl synthase / Thiolase/Chalcone synthase / Peroxisomal Thiolase; Chain A, domain 1 / Beta-ketoacyl synthase / 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 / 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
3,5,7,9,11-pentakis(oxidanylidene)dodecanal / Acyl carrier protein / Photorhabdus luminescens subsp. laumondii TTO1 complete genome segment 15/17 / Photorhabdus luminescens subsp. laumondii TTO1 complete genome segment 15/17 / Photorhabdus luminescens subsp. laumondii TTO1 complete genome segment 15/17
Similarity search - Component
Biological speciesPhotorhabdus luminescens (bacteria)
Photorhabdus luminescens subsp. laumondii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsBraeuer, A. / Zhou, Q. / Grammbitter, G.L.C. / Schmalhofer, M. / Ruehl, M. / Kaila, V.R.I. / Bode, H. / Groll, M.
CitationJournal: Nat.Chem. / Year: 2020
Title: Structural snapshots of the minimal PKS system responsible for octaketide biosynthesis.
Authors: Brauer, A. / Zhou, Q. / Grammbitter, G.L.C. / Schmalhofer, M. / Ruhl, M. / Kaila, V.R.I. / Bode, H.B. / Groll, M.
History
DepositionAug 22, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 27, 2020Provider: repository / Type: Initial release
Revision 1.1Jul 15, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Aug 5, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Nov 11, 2020Group: Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop
Revision 1.4Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Acyl carrier protein
B: PKS_KS domain-containing protein
C: Ketoacyl_synth_N domain-containing protein
D: PKS_KS domain-containing protein
E: Ketoacyl_synth_N domain-containing protein
F: PKS_KS domain-containing protein
G: Ketoacyl_synth_N domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)276,16913
Polymers275,2647
Non-polymers9056
Water2,594144
1
A: Acyl carrier protein
B: PKS_KS domain-containing protein
C: Ketoacyl_synth_N domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,2434
Polymers98,9893
Non-polymers2541
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: PKS_KS domain-containing protein
E: Ketoacyl_synth_N domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,4385
Polymers88,1382
Non-polymers3003
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
F: PKS_KS domain-containing protein
G: Ketoacyl_synth_N domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,4884
Polymers88,1382
Non-polymers3502
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)107.650, 107.650, 201.330
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number76
Space group name H-MP41

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Components

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Protein , 3 types, 7 molecules ABDFCEG

#1: Protein Acyl carrier protein


Mass: 10850.877 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Photorhabdus luminescens (bacteria) / Gene: C6H68_21855 / Plasmid: plasmid / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A2S8QL96, UniProt: Q7MZT5*PLUS
#2: Protein PKS_KS domain-containing protein


Mass: 47350.023 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Photorhabdus luminescens subsp. laumondii (strain DSM 15139 / CIP 105565 / TT01) (bacteria)
Gene: plu4191 / Plasmid: plasmid / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q7MZT3
#3: Protein Ketoacyl_synth_N domain-containing protein


Mass: 40787.746 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Photorhabdus luminescens subsp. laumondii (strain DSM 15139 / CIP 105565 / TT01) (bacteria)
Gene: plu4190 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q7MZT4

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Non-polymers , 4 types, 150 molecules

#4: Chemical ChemComp-LKZ / 3,5,7,9,11-pentakis(oxidanylidene)dodecanal


Mass: 254.236 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C12H14O6
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#6: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 144 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.29 Å3/Da / Density % sol: 46.24 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.2 / Details: 0.1 M BIS-TRIS, 0.4 M (NH4)2SO4, 29% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 16, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. obs: 61596 / % possible obs: 98.2 % / Redundancy: 2.9 % / CC1/2: 0.99 / Rmerge(I) obs: 0.123 / Net I/σ(I): 8.8
Reflection shellResolution: 2.7→2.8 Å / Rmerge(I) obs: 0.59 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 6401 / CC1/2: 0.663

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6SM4, 1TQY

6sm4

1tqy


Resolution: 2.7→30 Å / Cor.coef. Fo:Fc: 0.917 / Cor.coef. Fo:Fc free: 0.878 / SU B: 37.074 / SU ML: 0.325 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.416
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2648 3077 5 %RANDOM
Rwork0.2257 ---
obs0.2289 58463 98.16 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 139.39 Å2 / Biso mean: 42.297 Å2 / Biso min: 18.5 Å2
Baniso -1Baniso -2Baniso -3
1-0.89 Å2-0 Å20 Å2
2--0.89 Å20 Å2
3----1.78 Å2
Refinement stepCycle: final / Resolution: 2.7→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17923 0 7 144 18074
Biso mean--59.87 31.22 -
Num. residues----2351
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0020.01318242
X-RAY DIFFRACTIONr_bond_other_d0.0020.01716761
X-RAY DIFFRACTIONr_angle_refined_deg1.1871.63124653
X-RAY DIFFRACTIONr_angle_other_deg1.11.57838915
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.19652335
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.70223.292896
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.664153051
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.9971588
X-RAY DIFFRACTIONr_chiral_restr0.0350.22427
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.0220716
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023720
X-RAY DIFFRACTIONr_rigid_bond_restr0.149335003
LS refinement shellResolution: 2.7→2.77 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.343 226 -
Rwork0.306 4309 -
all-4535 -
obs--98.82 %
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)
10.6562-1.32781.06414.277-1.25992.88590.0744-0.30040.0217-0.4390.5596-0.5255-0.0585-0.2671-0.6340.0591-0.04990.11120.2266-0.14060.375-16.209397.96437.1171
20.29980.0607-0.16140.1936-0.03730.35780.01450.0188-0.0130.0444-0.0401-0.05010.013-0.03250.02570.1401-0.0117-0.02110.05140.01950.1519-36.618269.6449-5.5154
30.187-0.01010.06950.34840.00520.5742-0.02260.05250.0171-0.0404-0.0222-0.0457-0.06510.02330.04470.1182-0.0387-0.00520.08090.01430.1468-27.321682.7455-28.4766
40.3413-0.15780.13510.086-0.08730.4626-0.00740.0174-0.0034-0.0085-0.0014-0.0153-0.02320.00040.00880.1213-0.0109-0.01260.0790.00910.1425-52.099931.0576-3.7686
50.50940.1192-0.05520.0399-0.00510.62050.013-0.0522-0.01470.0042-0.0083-0.00150.0572-0.0095-0.00470.12970.01-0.01670.06520.00110.1387-54.536414.969619.1467
60.2311-0.1684-0.01690.20650.14780.5724-0.021-0.0006-0.0199-0.03180.02040.00770.062-0.02970.00050.0846-0.02910.03120.0861-0.0130.1659-107.825620.7008-1.1929
70.29050.09970.05370.2080.08190.4368-0.0023-0.0484-0.00030.01190.0181-0.0084-0.0239-0.0067-0.01580.099-0.00710.04130.0920.00290.1522-104.389638.776620.2177
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A6 - 76
2X-RAY DIFFRACTION2B10 - 425
3X-RAY DIFFRACTION3C2 - 371
4X-RAY DIFFRACTION4D10 - 427
5X-RAY DIFFRACTION5E1 - 371
6X-RAY DIFFRACTION6F10 - 426
7X-RAY DIFFRACTION7G1 - 371

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