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- PDB-6iyo: Crystal Structure of the acyltransferase domain from the second m... -

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Basic information

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


phosphopantetheine binding / 3-oxoacyl-[acyl-carrier-protein] synthase activity / antibiotic biosynthetic process / fatty acid biosynthetic process / oxidoreductase activity
Similarity search - Function
Polyketide synthase dehydratase N-terminal domain / PKS_DH / Polyketide synthase, dehydratase domain / Polyketide synthase, dehydratase domain superfamily / Polyketide synthase, ketoreductase domain / KR domain / Malonyl-CoA ACP transacylase, ACP-binding / Polyketide synthase, C-terminal extension / Ketoacyl-synthetase C-terminal extension / Acyl transferase domain superfamily ...Polyketide synthase dehydratase N-terminal domain / PKS_DH / Polyketide synthase, dehydratase domain / Polyketide synthase, dehydratase domain superfamily / Polyketide synthase, ketoreductase domain / KR domain / Malonyl-CoA ACP transacylase, ACP-binding / Polyketide synthase, C-terminal extension / Ketoacyl-synthetase C-terminal extension / Acyl transferase domain superfamily / Acyl transferase / Acyl transferase domain / Acyl transferase domain in polyketide synthase (PKS) enzymes. / Acyl transferase/acyl hydrolase/lysophospholipase / Alcohol dehydrogenase, N-terminal / Alcohol dehydrogenase GroES-like domain / Polyketide synthase, enoylreductase domain / Enoylreductase / Polyketide synthase, phosphopantetheine-binding domain / Phosphopantetheine attachment site / Beta-ketoacyl synthase / Beta-ketoacyl synthase, active site / Ketosynthase family 3 (KS3) active site signature. / 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 / 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
Type I modular polyketide synthase
Similarity search - Component
Biological speciesStreptomyces albus subsp. albus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 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 10, 2019Provider: repository / Type: Initial release
Revision 1.1Jul 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 1.2Nov 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

Downloads & links

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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)98,1962
Polymers98,1962
Non-polymers00
Water64936
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7480 Å2
ΔGint-51 kcal/mol
Surface area33620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.093, 73.367, 248.000
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1010A21 - 436
2010B21 - 436

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Components

#1: Protein Type I modular polyketide synthase


Mass: 49098.109 Da / Num. of mol.: 2 / Fragment: UNP residues 3201-3642
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces albus subsp. albus (bacteria)
Gene: salAI / Plasmid: pET28a / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: H1ZZT3
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 36 / 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: 2.27 Å3/Da / Density % sol: 45.91 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 7.5 / Details: 0.1M Tris pH 7.5, 0.2M NaCl, 23% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9792 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: May 15, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 40302 / % possible obs: 90.7 % / Redundancy: 7.2 % / Rmerge(I) obs: 0.087 / Net I/σ(I): 21.7
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 7.5 % / Rmerge(I) obs: 0.506 / Mean I/σ(I) obs: 4.7 / Num. unique obs: 2767 / % possible all: 87.9

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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: 2.2→50 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.921 / SU B: 14.648 / SU ML: 0.173 / Cross valid method: THROUGHOUT / ESU R: 0.322 / ESU R Free: 0.236 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26 2111 5 %RANDOM
Rwork0.219 ---
obs0.221 40302 90.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 51.22 Å2
Baniso -1Baniso -2Baniso -3
1-1.93 Å20 Å20 Å2
2---2.37 Å20 Å2
3---0.44 Å2
Refinement stepCycle: LAST / Resolution: 2.2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6232 0 0 36 6268
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0196308
X-RAY DIFFRACTIONr_bond_other_d0.0020.026048
X-RAY DIFFRACTIONr_angle_refined_deg1.1461.9618578
X-RAY DIFFRACTIONr_angle_other_deg0.754313772
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.3815832
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.91322.143280
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.2415934
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.7311576
X-RAY DIFFRACTIONr_chiral_restr0.080.2976
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.0217348
X-RAY DIFFRACTIONr_gen_planes_other0.0060.021490
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_it4.2263.4843336
X-RAY DIFFRACTIONr_mcbond_other4.2243.4833335
X-RAY DIFFRACTIONr_mcangle_it5.9465.2064164
X-RAY DIFFRACTIONr_mcangle_other5.9475.2064165
X-RAY DIFFRACTIONr_scbond_it5.6264.1922971
X-RAY DIFFRACTIONr_scbond_other5.6254.1922972
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other8.4455.9934414
X-RAY DIFFRACTIONr_long_range_B_refined11.4333.70826015
X-RAY DIFFRACTIONr_long_range_B_other11.4333.70426004
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 21387 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.16 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.2→2.26 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.312 168 -
Rwork0.262 2767 -
obs--85.87 %
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)
10.0349-0.0321-0.02490.7641-0.20480.13570.05780.0409-0.0424-0.0367-0.10520.0718-0.0089-0.00430.04740.11920.0844-0.00130.08360.00790.1894-16.461632.4361-18.9724
20.21090.1776-0.15020.25120.00510.3262-0.07240.13330.0353-0.06470.09920.00310.0304-0.0884-0.02680.13910.073-0.01680.22280.01720.0586-9.087947.7941-48.6652
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A21 - 421
2X-RAY DIFFRACTION2B21 - 418

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