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- PDB-8in9: The structure of the GfsA KSQ-AT didomain in complex with the Gfs... -

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Basic information

Entry
Database: PDB / ID: 8in9
TitleThe structure of the GfsA KSQ-AT didomain in complex with the GfsA ACP domain
Components(Polyketide synthase) x 2
KeywordsLYASE / Decarboxylase / Complex / Polyketide synthase
Function / homology
Function and homology information


DIM/DIP cell wall layer assembly / fatty acid synthase activity / phosphopantetheine binding / 3-oxoacyl-[acyl-carrier-protein] synthase activity / antibiotic biosynthetic process / fatty acid biosynthetic process / plasma membrane / cytoplasm
Similarity search - Function
Alpha-Beta Plaits - #3290 / Polyketide synthase dimerisation element domain / Polyketide synthase dimerisation element domain / Malonyl-Coenzyme A Acyl Carrier Protein, domain 2 / Malonyl-Coenzyme A Acyl Carrier Protein; domain 2 / : / Polyketide synthase dehydratase N-terminal domain / Polyketide synthase, dehydratase domain / PKS_DH / : ...Alpha-Beta Plaits - #3290 / Polyketide synthase dimerisation element domain / Polyketide synthase dimerisation element domain / Malonyl-Coenzyme A Acyl Carrier Protein, domain 2 / Malonyl-Coenzyme A Acyl Carrier Protein; domain 2 / : / Polyketide synthase dehydratase N-terminal domain / Polyketide synthase, dehydratase domain / PKS_DH / : / Polyketide synthase dehydratase domain / PKS_PP_betabranch / Polyketide synthase, dehydratase domain superfamily / : / Polyketide and metazoan fatty acid synthase dehydratase (PKS/mFAS DH) domain profile. / Polyketide synthase, C-terminal extension / Ketoacyl-synthetase C-terminal extension / Polyketide synthase, ketoreductase domain / KR domain / Malonyl-CoA ACP transacylase, ACP-binding / : / Acyl transferase / Acyl transferase domain / Acyl transferase domain in polyketide synthase (PKS) enzymes. / Acyl transferase domain superfamily / Acyl transferase/acyl hydrolase/lysophospholipase / Thiolase/Chalcone synthase / Peroxisomal Thiolase; Chain A, domain 1 / Polyketide synthase, phosphopantetheine-binding domain / Phosphopantetheine attachment site / PKS_KR / Beta-ketoacyl synthase, active site / Ketosynthase family 3 (KS3) active site signature. / 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 / Phosphopantetheine attachment site. / Phosphopantetheine attachment site / ACP-like superfamily / Carrier protein (CP) domain profile. / Phosphopantetheine binding ACP domain / Alpha-Beta Plaits / NAD(P)-binding domain superfamily / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-9EF / Polyketide synthase
Similarity search - Component
Biological speciesStreptomyces graminofaciens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.4 Å
AuthorsChisuga, T. / Murakami, S. / Miyanaga, A. / Kudo, F. / Eguchi, T.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)20H02911 Japan
CitationJournal: Acs Chem.Biol. / Year: 2023
Title: Structure-Based Analysis of Transient Interactions between Ketosynthase-like Decarboxylase and Acyl Carrier Protein in a Loading Module of Modular Polyketide Synthase.
Authors: Chisuga, T. / Murakami, S. / Miyanaga, A. / Kudo, F. / Eguchi, T.
History
DepositionMar 9, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 31, 2023Provider: repository / Type: Initial release
Revision 1.1Jun 28, 2023Group: 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 1.2Nov 20, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Polyketide synthase
B: Polyketide synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)105,5243
Polymers105,1402
Non-polymers3831
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)102.212, 102.212, 408.013
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number98
Space group name H-MI4122
Space group name HallI4bw2bw
Symmetry operation#1: x,y,z
#2: -y+1/2,x,z+3/4
#3: y+1/2,-x,z+3/4
#4: x+1/2,-y,-z+3/4
#5: -x+1/2,y,-z+3/4
#6: -x,-y,z
#7: y,x,-z
#8: -y,-x,-z
#9: x+1/2,y+1/2,z+1/2
#10: -y+1,x+1/2,z+5/4
#11: y+1,-x+1/2,z+5/4
#12: x+1,-y+1/2,-z+5/4
#13: -x+1,y+1/2,-z+5/4
#14: -x+1/2,-y+1/2,z+1/2
#15: y+1/2,x+1/2,-z+1/2
#16: -y+1/2,-x+1/2,-z+1/2

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Components

#1: Protein Polyketide synthase


Mass: 94895.852 Da / Num. of mol.: 1 / Mutation: Q197C
Source method: isolated from a genetically manipulated source
Details: GB BAJ16467.2 / Source: (gene. exp.) Streptomyces graminofaciens (bacteria) / Gene: gfsA / Plasmid: pColdI / Production host: Escherichia coli BL21(DE3) (bacteria)
#2: Protein Polyketide synthase / acyl carrier protein


Mass: 10244.458 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces graminofaciens (bacteria) / Gene: gfsA / Plasmid: pColdI / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: E0D202
#3: Chemical ChemComp-9EF / N-[2-(acetylamino)ethyl]-N~3~-[(2R)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alaninamide


Mass: 383.335 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H26N3O8P / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationY

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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: 2.59 Å3/Da / Density % sol: 52.57 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: ammonium sulfate, Tris-HCl, Pentaerythritol ethoxylate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 4, 2022
RadiationMonochromator: Numerical link type Si(111) double crystal monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.4→50 Å / Num. obs: 15447 / % possible obs: 99.7 % / Redundancy: 10.3 % / Biso Wilson estimate: 154.88 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.063 / Net I/σ(I): 19.4
Reflection shellResolution: 3.4→3.67 Å / Redundancy: 10.8 % / Rmerge(I) obs: 1.334 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 3126 / CC1/2: 0.756 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.4→43.33 Å / SU ML: 0.4967 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 36.7828
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.3107 776 5.04 %
Rwork0.2652 14627 -
obs0.2674 15403 99.48 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 259.18 Å2
Refinement stepCycle: LAST / Resolution: 3.4→43.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6574 0 24 0 6598
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00446714
X-RAY DIFFRACTIONf_angle_d0.72459124
X-RAY DIFFRACTIONf_chiral_restr0.04611057
X-RAY DIFFRACTIONf_plane_restr0.00591197
X-RAY DIFFRACTIONf_dihedral_angle_d2.98713960
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.4-3.610.40811440.36052377X-RAY DIFFRACTION99.88
3.61-3.890.33711340.30042373X-RAY DIFFRACTION99.48
3.89-4.280.28421110.26632418X-RAY DIFFRACTION99.84
4.28-4.90.31011300.262420X-RAY DIFFRACTION99.57
4.9-6.170.29761200.31132466X-RAY DIFFRACTION99.61
6.17-43.330.30761370.23752573X-RAY DIFFRACTION98.58
Refinement TLS params.Method: refined / Origin x: 34.194556956 Å / Origin y: 34.9233838413 Å / Origin z: -28.6437801133 Å
111213212223313233
T2.04978602308 Å20.933784108101 Å20.207816089753 Å2-2.02276156108 Å20.201901515249 Å2--1.6991330508 Å2
L2.54940052159 °2-0.897186571758 °2-0.762076989196 °2-2.29523366068 °21.23595829828 °2--1.50869715572 °2
S0.355013474243 Å °1.23802175693 Å °0.369775348594 Å °-0.882353628135 Å °-0.167219017283 Å °-0.449400034132 Å °-0.616396022273 Å °-0.607311780933 Å °-0.113433486842 Å °
Refinement TLS groupSelection details: all

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