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- PDB-6iyt: Crystal Structure of the acyltransferase domain from second modul... -

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Basic information

Entry
Database: PDB / ID: 6iyt
TitleCrystal Structure of the acyltransferase domain from second module 14 of salinomycin polyketide synthase
ComponentsType I modular polyketide synthase
KeywordsTRANSFERASE / acyltransferase / ethylhmalonyl-coenzyme A / polyketide
Function / homology
Function and homology information


macrolide biosynthetic process / DIM/DIP cell wall layer assembly / fatty acid synthase activity / phosphopantetheine binding / 3-oxoacyl-[acyl-carrier-protein] synthase activity / fatty acid biosynthetic process / plasma membrane / cytoplasm
Similarity search - Function
Polyketide synthase dimerisation element domain / Polyketide synthase dimerisation element domain / Polyketide synthase, docking domain / Erythronolide synthase docking domain / PKS_PP_betabranch / Polyketide synthase, C-terminal extension / Ketoacyl-synthetase C-terminal extension / Polyketide synthase, ketoreductase domain / KR domain / Malonyl-CoA ACP transacylase, ACP-binding ...Polyketide synthase dimerisation element domain / Polyketide synthase dimerisation element domain / Polyketide synthase, docking domain / Erythronolide synthase docking domain / PKS_PP_betabranch / 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 / Polyketide synthase, phosphopantetheine-binding domain / Phosphopantetheine attachment site / Beta-ketoacyl synthase / Beta-ketoacyl synthase, active site / Ketosynthase family 3 (KS3) active site signature. / PKS_KR / 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 / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
Type I modular polyketide synthase
Similarity search - Component
Biological speciesStreptomyces albus subsp. albus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.78 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
B: Type I modular polyketide synthase


Theoretical massNumber of molelcules
Total (without water)97,5792
Polymers97,5792
Non-polymers00
Water7,909439
1
A: Type I modular polyketide synthase


Theoretical massNumber of molelcules
Total (without water)48,7901
Polymers48,7901
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Type I modular polyketide synthase


Theoretical massNumber of molelcules
Total (without water)48,7901
Polymers48,7901
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)120.818, 78.474, 106.714
Angle α, β, γ (deg.)90.00, 117.00, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Type I modular polyketide synthase


Mass: 48789.512 Da / Num. of mol.: 2 / Fragment: UNP residues 465-910
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces albus subsp. albus (bacteria)
Gene: salAIX / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): DE3 / References: UniProt: H1ZZU1
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 439 / 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: 2.43 Å3/Da / Density % sol: 49.28 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 8 / Details: 0.2M potassium acetate pH 8.0, 23% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97791 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Apr 26, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97791 Å / Relative weight: 1
ReflectionResolution: 1.78→50 Å / Num. obs: 80596 / % possible obs: 99.44 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.074 / Net I/σ(I): 17
Reflection shellResolution: 1.78→1.81 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.26 / Mean I/σ(I) obs: 4.2 / Num. unique obs: 5662 / % possible all: 99.7

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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: 1.78→50 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.93 / SU B: 2.285 / SU ML: 0.074 / Cross valid method: THROUGHOUT / ESU R: 0.116 / ESU R Free: 0.112 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21421 4244 5 %RANDOM
Rwork0.17943 ---
obs0.18117 80596 99.44 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 13.495 Å2
Baniso -1Baniso -2Baniso -3
1-0.61 Å2-0 Å2-0.48 Å2
2---0.12 Å2-0 Å2
3---0.01 Å2
Refinement stepCycle: 1 / Resolution: 1.78→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6293 0 0 439 6732
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0196435
X-RAY DIFFRACTIONr_bond_other_d00.026147
X-RAY DIFFRACTIONr_angle_refined_deg1.0541.9528782
X-RAY DIFFRACTIONr_angle_other_deg0.653314062
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.175855
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.60923.295261
X-RAY DIFFRACTIONr_dihedral_angle_3_deg1615942
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.2031552
X-RAY DIFFRACTIONr_chiral_restr0.0910.21037
X-RAY DIFFRACTIONr_gen_planes_refined0.0170.0217441
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021443
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_it1.9651.1313432
X-RAY DIFFRACTIONr_mcbond_other1.9561.133431
X-RAY DIFFRACTIONr_mcangle_it2.6131.6874283
X-RAY DIFFRACTIONr_mcangle_other2.6131.6884284
X-RAY DIFFRACTIONr_scbond_it3.581.4983002
X-RAY DIFFRACTIONr_scbond_other3.5791.4983003
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.3362.0964500
X-RAY DIFFRACTIONr_long_range_B_refined6.4229.9987548
X-RAY DIFFRACTIONr_long_range_B_other6.4169.8667397
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.779→1.825 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.248 279 -
Rwork0.192 5662 -
obs--94.65 %

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