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- PDB-6smp: AntDE:AntF (holo): type II PKS acyl-carrier protein in complex wi... -

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Basic information

Entry
Database: PDB / ID: 6smp
TitleAntDE:AntF (holo): 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


acyltransferase activity, transferring groups other than amino-acyl groups
Similarity search - Function
Beta-ketoacyl synthase / Thiolase/Chalcone synthase / Peroxisomal Thiolase; Chain A, domain 1 / Beta-ketoacyl synthase / 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 / Thiolase-like ...Beta-ketoacyl synthase / Thiolase/Chalcone synthase / Peroxisomal Thiolase; Chain A, domain 1 / Beta-ketoacyl synthase / 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 / 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-LLE / 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: 2.9 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 / Derived calculations / Category: citation / citation_author / struct_conn
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID / _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
Revision 1.3Jan 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: Acyl carrier protein
E: PKS_KS domain-containing protein
F: Ketoacyl_synth_N domain-containing protein
G: Acyl carrier protein
H: PKS_KS domain-containing protein
I: Ketoacyl_synth_N domain-containing protein
J: Acyl carrier protein
K: PKS_KS domain-containing protein
L: Ketoacyl_synth_N domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)398,41316
Polymers395,95512
Non-polymers2,4584
Water1,45981
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)99,6034
Polymers98,9893
Non-polymers6151
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: Acyl carrier protein
E: PKS_KS domain-containing protein
F: Ketoacyl_synth_N domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,6034
Polymers98,9893
Non-polymers6151
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
G: Acyl carrier protein
H: PKS_KS domain-containing protein
I: Ketoacyl_synth_N domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,6034
Polymers98,9893
Non-polymers6151
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
J: Acyl carrier protein
K: PKS_KS domain-containing protein
L: Ketoacyl_synth_N domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,6034
Polymers98,9893
Non-polymers6151
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)108.300, 135.940, 148.600
Angle α, β, γ (deg.)90.000, 97.140, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Acyl carrier protein /


Mass: 10850.877 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Photorhabdus luminescens (bacteria) / Gene: C6H68_21855 / 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.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Photorhabdus luminescens subsp. laumondii (strain DSM 15139 / CIP 105565 / TT01) (bacteria)
Strain: DSM 15139 / CIP 105565 / TT01 / Gene: plu4191 / 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.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Photorhabdus luminescens subsp. laumondii (strain DSM 15139 / CIP 105565 / TT01) (bacteria)
Strain: DSM 15139 / CIP 105565 / TT01 / Gene: plu4190 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q7MZT4
#4: Chemical
ChemComp-LLE / (2~{R})-3,3-dimethyl-2-oxidanyl-~{N}-[3-oxidanylidene-3-[2-[(1~{R},4~{Z},6~{Z},8~{Z})-1,5,7,9-tetrakis(oxidanyl)-3,11-bis(oxidanylidene)dodeca-4,6,8-trienyl]sulfanylethylamino]propyl]-4-[tris(oxidanyl)-$l^{5}-phosphanyl]oxy-butanamide


Mass: 614.600 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C23H39N2O13PS
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 81 / Source method: isolated from a natural source / Formula: H2O
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: 2.99 Å3/Da / Density % sol: 58.84 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: 0.1 M BIS-TRIS, 0.5 M (NH4)2SO4, 30% 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: Oct 15, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.9→50 Å / Num. obs: 92717 / % possible obs: 97.9 % / Redundancy: 3.1 % / CC1/2: 0.993 / Rmerge(I) obs: 0.097 / Net I/σ(I): 11.4
Reflection shellResolution: 2.9→3 Å / Rmerge(I) obs: 0.543 / Mean I/σ(I) obs: 2.4 / Num. unique obs: 8962 / CC1/2: 0.734 / % possible all: 98.4

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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: 6SMO

6smo


Resolution: 2.9→15 Å / Cor.coef. Fo:Fc: 0.919 / Cor.coef. Fo:Fc free: 0.896 / SU B: 44.249 / SU ML: 0.357 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.417 / Details: U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.258 4600 5 %RANDOM
Rwork0.2217 ---
obs0.2236 87419 97.17 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 149.74 Å2 / Biso mean: 61.457 Å2 / Biso min: 24.64 Å2
Baniso -1Baniso -2Baniso -3
1-4.29 Å20 Å2-0.49 Å2
2---2.79 Å2-0 Å2
3----1.33 Å2
Refinement stepCycle: final / Resolution: 2.9→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms25620 0 0 81 25701
Biso mean---52.45 -
Num. residues----3338
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0020.01226069
X-RAY DIFFRACTIONr_angle_refined_deg0.8271.68335243
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.24253313
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.80123.4461297
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.597154053
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.18715124
X-RAY DIFFRACTIONr_chiral_restr0.0720.23475
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.0219866
X-RAY DIFFRACTIONr_rigid_bond_restr0.129326069
LS refinement shellResolution: 2.9→2.972 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.401 331 -
Rwork0.375 6291 -
all-6622 -
obs--98.32 %
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)
10.64250.11370.65140.0394-0.02041.71340.04390.0665-0.0074-0.00820.01850.02220.16-0.0507-0.06250.0446-0.0295-0.02040.1592-0.04590.16064.95-35.582.8663
20.0608-0.0114-0.01450.06660.06040.05750.00290.00270.00370.0053-0.01790.00570.0153-0.00580.01490.1111-0.0027-0.00570.1816-0.00640.153331.9374-16.733721.4394
30.0013-0.0039-0.00630.09840.03710.0646-0.00550.00170.0027-0.0246-0.02030.0027-0.0226-0.01680.02580.10850.0081-0.02070.1844-0.0130.155119.55592.38795.1756
41.2124-0.3925-0.53510.13250.17650.23990.09680.0420.1464-0.0246-0.0366-0.0242-0.04-0.0449-0.06020.060.00410.01590.202-0.04320.1745-2.141743.795458.2347
50.05340.00950.00230.06960.05770.05640.0060.00420.00220.0092-0.01650.0009-0.0047-0.00870.01060.1032-0.0003-0.00790.1851-0.0060.150328.605924.676947.3687
60.01570.0117-0.02760.08980.00780.0627-0.00990.0092-0.00010.0293-0.01650.01460.0366-0.01610.02640.1153-0.01370.00740.1813-0.01690.152112.41195.644359.933
71.45060.4224-0.64050.1616-0.39071.42550.0833-0.0413-0.00730.0324-0.0845-0.0077-0.04020.23410.00130.0159-0.0347-0.02110.18220.02980.149999.984149.663221.4269
80.0502-0.02220.01340.0931-0.05710.0574-0.004-0.0002-0.01280.01370.01070.0049-0.02790.0024-0.00670.1026-0.0009-0.00370.18490.00660.15264.936135.638427.0866
90.0014-0.0023-0.00250.1467-0.04360.0622-0.006-0.0072-0.0095-0.0243-0.0097-0.01290.01440.00760.01580.1056-0.0002-0.00180.18060.0110.155479.940514.415416.5532
100.8654-0.52860.64140.3343-0.38610.48530.05650.0170.056-0.0338-0.062-0.06260.0710.02060.00550.05350.0202-0.00840.21690.06530.124395.1416-41.387964.8217
110.07770.0167-0.03670.0951-0.02620.0834-0.006-0.00560.0065-0.0381-0.00970.01270.03240.00510.01570.12530.0047-0.01390.17430.01370.133762.8505-27.732950.2339
120.00250.00190.01320.19410.01520.0835-0.0042-0.00580.00410.0027-0.0096-0.0052-0.02060.01430.01370.1109-0.0024-0.01170.18070.01880.148874.2192-6.267564.3014
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A5 - 76
2X-RAY DIFFRACTION2B2 - 426
3X-RAY DIFFRACTION3C2 - 371
4X-RAY DIFFRACTION4D5 - 76
5X-RAY DIFFRACTION5E2 - 426
6X-RAY DIFFRACTION6F2 - 371
7X-RAY DIFFRACTION7G5 - 76
8X-RAY DIFFRACTION8H2 - 427
9X-RAY DIFFRACTION9I2 - 371
10X-RAY DIFFRACTION10J5 - 76
11X-RAY DIFFRACTION11K2 - 426
12X-RAY DIFFRACTION12L2 - 371

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