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- PDB-6iyr: Crystal Structure of the acyltransferase domain from module 8 of ... -

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Basic information

Entry
Database: PDB / ID: 6iyr
TitleCrystal Structure of the acyltransferase domain from module 8 of the salinomycin polyketide synthase
ComponentsType I modular polyketide synthase
KeywordsTRANSFERASE / acyltransferase / malonyl-coenzyme A / polyketide
Function / homology
Function and homology information


macrolide biosynthetic process / fatty acid synthase activity / phosphopantetheine binding / 3-oxoacyl-[acyl-carrier-protein] synthase activity / fatty acid biosynthetic process / oxidoreductase activity / zinc ion binding
Similarity search - Function
Polyketide synthase dimerisation element domain / Polyketide synthase dimerisation element domain / Quinone oxidoreductase/zeta-crystallin, conserved site / Quinone oxidoreductase / zeta-crystallin signature. / : / Polyketide synthase extender module SpnB, Rossmann fold domain / Polyketide synthase, docking domain / Erythronolide synthase docking domain / Zinc-binding dehydrogenase / : ...Polyketide synthase dimerisation element domain / Polyketide synthase dimerisation element domain / Quinone oxidoreductase/zeta-crystallin, conserved site / Quinone oxidoreductase / zeta-crystallin signature. / : / Polyketide synthase extender module SpnB, Rossmann fold domain / Polyketide synthase, docking domain / Erythronolide synthase docking domain / Zinc-binding dehydrogenase / : / 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 / Alcohol dehydrogenase, N-terminal / Alcohol dehydrogenase GroES-like domain / Acyl transferase/acyl hydrolase/lysophospholipase / Polyketide synthase, enoylreductase domain / Enoylreductase / 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 / GroES-like superfamily / Thiolase-like / Phosphopantetheine attachment site / Phosphopantetheine attachment site. / Phosphopantetheine attachment site / ACP-like superfamily / Carrier protein (CP) domain profile. / Phosphopantetheine binding ACP domain / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
PHOSPHATE ION / Type I modular polyketide synthase
Similarity search - Component
Biological speciesStreptomyces albus subsp. albus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsZhang, F. / Zheng, J.
Funding support China, 1items
OrganizationGrant numberCountry
National Science Foundation (China)31570056, 31770068 China
CitationJournal: Biochemistry / Year: 2019
Title: Structural Insights into the Substrate Specificity of Acyltransferases from Salinomycin Polyketide Synthase.
Authors: Zhang, F. / Shi, T. / Ji, H. / Ali, I. / Huang, S. / Deng, Z. / Min, Q. / Bai, L. / Zhao, Y. / Zheng, J.
History
DepositionDec 17, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 3, 2019Provider: repository / Type: Initial release
Revision 1.1Jul 10, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Jul 24, 2019Group: Data collection / 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 22, 2023Group: 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

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Assembly

Deposited unit
A: Type I modular polyketide synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,0932
Polymers48,9981
Non-polymers951
Water1,58588
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area220 Å2
ΔGint-8 kcal/mol
Surface area16730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)123.244, 123.244, 78.532
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Space group name H-MP42212

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Components

#1: Protein Type I modular polyketide synthase


Mass: 48997.930 Da / Num. of mol.: 1 / Fragment: UNP residues 480-929
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces albus subsp. albus (bacteria)
Gene: salAV / Plasmid: pET28a / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: H1ZZT7
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


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


Mass: 18.015 Da / Num. of mol.: 88 / Source method: isolated from a natural source / Formula: H2O

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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: 3.04 Å3/Da / Density % sol: 59.58 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 8.2 / Details: 0.056M NaH2PO4, 1.544M K2HPO4 pH 8.2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97914 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: May 27, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97914 Å / Relative weight: 1
ReflectionResolution: 2.05→50 Å / Num. obs: 36404 / % possible obs: 99.93 % / Redundancy: 14.5 % / Rmerge(I) obs: 0.087 / Net I/σ(I): 56.4
Reflection shellResolution: 2.05→2.09 Å / Redundancy: 14.6 % / Rmerge(I) obs: 0.66 / Mean I/σ(I) obs: 5.3 / Num. unique obs: 2628 / % possible all: 99.68

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2HG4

2hg4


Resolution: 2.05→50 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.935 / SU B: 4.054 / SU ML: 0.109 / Cross valid method: THROUGHOUT / ESU R: 0.153 / ESU R Free: 0.149 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24166 1901 5 %RANDOM
Rwork0.20114 ---
obs0.20316 36404 99.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 37.968 Å2
Baniso -1Baniso -2Baniso -3
1--0.43 Å20 Å20 Å2
2---0.43 Å2-0 Å2
3---0.86 Å2
Refinement stepCycle: 1 / Resolution: 2.05→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3098 0 5 88 3191
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0193133
X-RAY DIFFRACTIONr_bond_other_d00.023006
X-RAY DIFFRACTIONr_angle_refined_deg1.5161.9564280
X-RAY DIFFRACTIONr_angle_other_deg0.79236866
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2025418
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.40422.857126
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.5515453
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.6481530
X-RAY DIFFRACTIONr_chiral_restr0.1210.2502
X-RAY DIFFRACTIONr_gen_planes_refined0.0160.0213623
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02695
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it4.493.4091678
X-RAY DIFFRACTIONr_mcbond_other4.4863.4081677
X-RAY DIFFRACTIONr_mcangle_it5.0415.0782094
X-RAY DIFFRACTIONr_mcangle_other5.0425.082095
X-RAY DIFFRACTIONr_scbond_it7.474.1021455
X-RAY DIFFRACTIONr_scbond_other7.3284.0961452
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other9.7935.8752181
X-RAY DIFFRACTIONr_long_range_B_refined10.44628.1183564
X-RAY DIFFRACTIONr_long_range_B_other10.46328.0893545
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.053→2.106 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.308 139 -
Rwork0.265 2628 -
obs--99.68 %

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