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- PDB-6kxe: The ishigamide ketosynthase/chain length factor -

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Basic information

Entry
Database: PDB / ID: 6kxe
TitleThe ishigamide ketosynthase/chain length factor
Components(KetosynthaseKetoacyl synthase) x 2
KeywordsTRANSFERASE / polyketide synthase
Function / homology
Function and homology information


acyltransferase activity, transferring groups other than amino-acyl groups / fatty acid biosynthetic process
Similarity search - Function
Beta-ketoacyl synthase / Thiolase/Chalcone synthase / Peroxisomal Thiolase; Chain A, domain 1 / Ketosynthase family 3 (KS3) domain profile. / 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 ...Beta-ketoacyl synthase / Thiolase/Chalcone synthase / Peroxisomal Thiolase; Chain A, domain 1 / Ketosynthase family 3 (KS3) domain profile. / 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 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / PHOSPHATE ION / PROPANOIC ACID / Ketosynthase / Ketosynthase
Similarity search - Component
Biological speciesStreptomyces sp. MSC090213JE08 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.81 Å
AuthorsDu, D. / Katsuyama, Y. / Horiuchi, M. / Fushinobu, S. / Chen, A. / Davis, T. / Burkart, M. / Ohnishi, Y.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of ScienceJP25108706 Japan
CitationJournal: Nat.Chem.Biol. / Year: 2020
Title: Structural basis for selectivity in a highly reducing type II polyketide synthase.
Authors: Du, D. / Katsuyama, Y. / Horiuchi, M. / Fushinobu, S. / Chen, A. / Davis, T.D. / Burkart, M.D. / Ohnishi, Y.
History
DepositionSep 10, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 6, 2020Provider: repository / Type: Initial release
Revision 1.1May 20, 2020Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 2.0Jun 17, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Author supporting evidence / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_entity_instance_feature / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_unobs_or_zero_occ_atoms / struct_conn / struct_site
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _pdbx_entity_instance_feature.auth_comp_id / _pdbx_entity_instance_feature.comp_id / _pdbx_entity_nonpoly.comp_id / _pdbx_entity_nonpoly.name / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.pdb_mon_id / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_site.details / _struct_site.pdbx_auth_comp_id
Revision 2.1Jul 8, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ketosynthase
B: Ketosynthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,5906
Polymers81,3002
Non-polymers2904
Water9,440524
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6760 Å2
ΔGint-31 kcal/mol
Surface area23850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.426, 69.426, 265.465
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11B-651-

HOH

21B-730-

HOH

31B-746-

HOH

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein Ketosynthase / Ketoacyl synthase


Mass: 42747.785 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces sp. MSC090213JE08 (bacteria)
Gene: iga11 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A1Y1BW67
#2: Protein Ketosynthase / Ketoacyl synthase


Mass: 38552.477 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces sp. MSC090213JE08 (bacteria)
Gene: iga12 / Plasmid: pColdI / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A1Y1BW66

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Non-polymers , 5 types, 528 molecules

#3: Chemical ChemComp-PPI / PROPANOIC ACID / Propionic acid


Mass: 74.079 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H6O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 524 / 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: 2.27 Å3/Da / Density % sol: 45.85 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 1.1 M sodium phosphate monobasic, 1.65 M potassium phosphate dibasic, and 0.1 M sodium acetate/acetic acid buffer

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Data collection

DiffractionMean temperature: 95 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 22, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.81→49.78 Å / Num. obs: 65008 / % possible obs: 99.7 % / Redundancy: 19.6 % / CC1/2: 0.999 / Rmerge(I) obs: 0.163 / Rpim(I) all: 0.052 / Rrim(I) all: 0.168 / Net I/σ(I): 12.8
Reflection shellResolution: 1.81→1.85 Å / Rmerge(I) obs: 2.012 / Num. unique obs: 3883 / CC1/2: 0.61 / Rpim(I) all: 0.698 / Rrim(I) all: 2.075

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
PHENIXrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.81→49.78 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.953 / SU B: 2.848 / SU ML: 0.084 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.116 / ESU R Free: 0.119
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2116 3333 4.9 %RANDOM
Rwork0.1633 ---
obs0.1656 65008 99.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 87.31 Å2 / Biso mean: 27.944 Å2 / Biso min: 13.19 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: final / Resolution: 1.81→49.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5498 0 17 524 6039
Biso mean--44.5 38.66 -
Num. residues----759
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0135600
X-RAY DIFFRACTIONr_bond_other_d0.0010.0175272
X-RAY DIFFRACTIONr_angle_refined_deg1.631.6377616
X-RAY DIFFRACTIONr_angle_other_deg1.4931.57512119
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8255757
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.72320.559286
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.71315828
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.8821555
X-RAY DIFFRACTIONr_chiral_restr0.0810.2755
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.026536
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021197
LS refinement shellResolution: 1.814→1.861 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.311 249 -
Rwork0.278 4606 -
all-4855 -
obs--97.94 %

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