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- PDB-6smd: PlMCAT:AntF (holo): type II PKS acyl-carrier protein in complex w... -

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Basic information

Entry
Database: PDB / ID: 6smd
TitlePlMCAT:AntF (holo): type II PKS acyl-carrier protein in complex with its malonyl-transacylase
Components
  • Acyl carrier protein
  • Malonyl CoA-acyl carrier protein transacylase
KeywordsPROTEIN BINDING / Natural Product Biosynthesis / Polyketides / Minimal PKS System / Anthraquinone / Chain Elongation / Catalysis
Function / homology
Function and homology information


[acyl-carrier-protein] S-malonyltransferase / [acyl-carrier-protein] S-malonyltransferase activity / fatty acid biosynthetic process
Similarity search - Function
Malonyl CoA-acyl carrier protein transacylase / Malonyl CoA-acyl carrier protein transacylase, FabD-type / Malonyl-CoA ACP transacylase, ACP-binding / Malonyl-Coenzyme A Acyl Carrier Protein, domain 2 / Malonyl-Coenzyme A Acyl Carrier Protein; domain 2 / Malonyl-CoA ACP transacylase, ACP-binding / Acyl transferase domain superfamily / Acyl transferase / Acyl transferase domain / Acyl transferase domain in polyketide synthase (PKS) enzymes. ...Malonyl CoA-acyl carrier protein transacylase / Malonyl CoA-acyl carrier protein transacylase, FabD-type / Malonyl-CoA ACP transacylase, ACP-binding / Malonyl-Coenzyme A Acyl Carrier Protein, domain 2 / Malonyl-Coenzyme A Acyl Carrier Protein; domain 2 / Malonyl-CoA ACP transacylase, ACP-binding / Acyl transferase domain superfamily / Acyl transferase / Acyl transferase domain / Acyl transferase domain in polyketide synthase (PKS) enzymes. / Acyl transferase/acyl hydrolase/lysophospholipase / Phosphopantetheine attachment site / ACP-like superfamily / Carrier protein (CP) domain profile. / Phosphopantetheine binding ACP domain / Alpha-Beta Plaits / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Acyl carrier protein / Malonyl CoA-acyl carrier protein transacylase
Similarity search - Component
Biological speciesPhotorhabdus luminescens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 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 21, 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 1.3Jan 24, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.name / _chem_comp.pdbx_synonyms ..._chem_comp.name / _chem_comp.pdbx_synonyms / _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: Malonyl CoA-acyl carrier protein transacylase
C: Malonyl CoA-acyl carrier protein transacylase


Theoretical massNumber of molelcules
Total (without water)77,4653
Polymers77,4653
Non-polymers00
Water0
1
A: Acyl carrier protein
B: Malonyl CoA-acyl carrier protein transacylase


Theoretical massNumber of molelcules
Total (without water)44,3282
Polymers44,3282
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Malonyl CoA-acyl carrier protein transacylase


Theoretical massNumber of molelcules
Total (without water)33,1371
Polymers33,1371
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)79.580, 84.600, 158.110
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Acyl carrier protein /


Mass: 11191.210 Da / Num. of mol.: 1
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
#2: Protein Malonyl CoA-acyl carrier protein transacylase


Mass: 33136.820 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Photorhabdus luminescens (bacteria) / Gene: fabD, plu2834 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q7N385, [acyl-carrier-protein] S-malonyltransferase
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: 3.54 Å3/Da / Density % sol: 65.3 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 1.8 M Na/K-phosphate, 4% polypropylene glycol P400

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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: Jun 30, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.3→50 Å / Num. obs: 16593 / % possible obs: 99.3 % / Redundancy: 4.7 % / CC1/2: 0.991 / Rmerge(I) obs: 0.133 / Net I/σ(I): 9.6
Reflection shellResolution: 3.3→3.4 Å / Rmerge(I) obs: 0.474 / Mean I/σ(I) obs: 3.6 / Num. unique obs: 1402 / CC1/2: 0.917

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2G1H

2g1h


Resolution: 3.3→30 Å / Cor.coef. Fo:Fc: 0.907 / Cor.coef. Fo:Fc free: 0.863 / SU B: 58.9 / SU ML: 0.423 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.53
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2715 827 5 %RANDOM
Rwork0.2321 ---
obs0.2332 15708 99.21 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 191.52 Å2 / Biso mean: 74.66 Å2 / Biso min: 30 Å2
Baniso -1Baniso -2Baniso -3
1--5.3 Å2-0 Å20 Å2
2--3.68 Å2-0 Å2
3---1.62 Å2
Refinement stepCycle: final / Resolution: 3.3→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5284 0 0 0 5284
Num. residues----697
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0195378
X-RAY DIFFRACTIONr_bond_other_d0.0010.025067
X-RAY DIFFRACTIONr_angle_refined_deg0.9811.9657314
X-RAY DIFFRACTIONr_angle_other_deg0.8473.00111758
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.575694
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.13725.677229
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.04315889
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.3881523
X-RAY DIFFRACTIONr_chiral_restr0.0490.2850
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0216037
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02998
X-RAY DIFFRACTIONr_rigid_bond_restr1.213310445
X-RAY DIFFRACTIONr_sphericity_bonded14.862510353
LS refinement shellResolution: 3.3→3.385 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.294 60 -
Rwork0.314 1142 -
all-1202 -
obs--99.59 %
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)
10.0025-0.0025-0.00290.0080.00430.0066-0.0142-0.0083-0.0147-0.0041-0.01240.0327-0.00520.01860.02660.14030.0154-0.03460.13230.03870.1775-2.676847.3583-10.9815
20.0341-0.02830.04190.031-0.03850.0549-0.00750.01440.02140.0116-0.00440.0154-0.00010.00750.01190.1315-0.00550.00290.0871-0.00340.188-21.427737.5683-29.8228
30.0589-0.0204-0.09080.01240.03660.14580.00910.00150.00130.02110.00130.00250.01010.0001-0.01050.11350.00270.00370.0879-0.00160.1874-26.12823.3778-23.1805
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 80
2X-RAY DIFFRACTION2B1 - 310
3X-RAY DIFFRACTION3C2 - 310

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