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- PDB-7uci: SxtA Methyltransferase and decarboxylase didomain in complex with... -

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Basic information

Entry
Database: PDB / ID: 7uci
TitleSxtA Methyltransferase and decarboxylase didomain in complex with Mn2+ and SAH
ComponentsPolyketide synthase-related protein
KeywordsTRANSFERASE / Methyltransferase
Function / homology
Function and homology information


biosynthetic process / phosphopantetheine binding / acetyltransferase activity / pyridoxal phosphate binding
Similarity search - Function
Polyketide synthase, phosphopantetheine-binding domain / Phosphopantetheine attachment site / Aminotransferase, class I/classII / Aminotransferase class I and II / Gcn5-related N-acetyltransferase (GNAT) domain profile. / GNAT domain / Acyl-CoA N-acyltransferase / Phosphopantetheine attachment site / ACP-like superfamily / Carrier protein (CP) domain profile. ...Polyketide synthase, phosphopantetheine-binding domain / Phosphopantetheine attachment site / Aminotransferase, class I/classII / Aminotransferase class I and II / Gcn5-related N-acetyltransferase (GNAT) domain profile. / GNAT domain / Acyl-CoA N-acyltransferase / Phosphopantetheine attachment site / ACP-like superfamily / Carrier protein (CP) domain profile. / Phosphopantetheine binding ACP domain / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
: / S-ADENOSYL-L-HOMOCYSTEINE / Polyketide synthase-related protein
Similarity search - Component
Biological speciesCylindrospermopsis raciborskii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsLao, Y. / Skiba, M.A. / Smith, J.L.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)DK042303 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)CA108874 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P30 GM138396 United States
CitationJournal: Acs Chem.Biol. / Year: 2022
Title: Structural Basis for Control of Methylation Extent in Polyketide Synthase Metal-Dependent C -Methyltransferases.
Authors: Lao, Y. / Skiba, M.A. / Chun, S.W. / Narayan, A.R.H. / Smith, J.L.
History
DepositionMar 16, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 1, 2022Provider: repository / Type: Initial release
Revision 1.1Aug 31, 2022Group: 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 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Polyketide synthase-related protein
B: Polyketide synthase-related protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)163,3457
Polymers162,3742
Non-polymers9715
Water1,56787
1
A: Polyketide synthase-related protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,6263
Polymers81,1871
Non-polymers4392
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Polyketide synthase-related protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,7184
Polymers81,1871
Non-polymers5313
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)43.802, 69.668, 127.608
Angle α, β, γ (deg.)86.440, 83.260, 83.950
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z

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Components

#1: Protein Polyketide synthase-related protein


Mass: 81187.008 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cylindrospermopsis raciborskii (bacteria)
Gene: sxtA / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: B3EYF9
#2: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H20N6O5S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 87 / Source method: isolated from a natural source / Formula: H2O
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: 2.37 Å3/Da / Density % sol: 48 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.25
Details: 12-14mg/mL SxtA MT-DC in 50mM Tris pH7.4, 50mM NaCl, 10%(v/v) glycerol, 5mM S-adenosyl-L-methionine (SAM), and 5mM MnCl2. Well solution: 5-8% PEG 20K, and 0.1M MES pH 6.25-6.5
PH range: 6.25-6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.033 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 12, 2019
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 2.6→42.43 Å / Num. obs: 44788 / % possible obs: 97.8 % / Redundancy: 3.6 % / Biso Wilson estimate: 51.19 Å2 / CC1/2: 0.995 / CC star: 0.999 / Rmerge(I) obs: 0.1261 / Net I/σ(I): 8.57
Reflection shellResolution: 2.6→2.69 Å / Redundancy: 3.5 % / Mean I/σ(I) obs: 1.39 / Num. unique obs: 4306 / CC1/2: 0.696 / CC star: 0.906 / % possible all: 94.19

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
JBluIce-EPICSdata collection
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6B3A

6b3a


Resolution: 2.6→42.43 Å / SU ML: 0.472 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 36.3255
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.298 3931 4.47 %
Rwork0.2375 84068 -
obs0.2402 44788 97.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 64.76 Å2
Refinement stepCycle: LAST / Resolution: 2.6→42.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10723 0 60 87 10870
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.002911031
X-RAY DIFFRACTIONf_angle_d0.651414983
X-RAY DIFFRACTIONf_chiral_restr0.04231696
X-RAY DIFFRACTIONf_plane_restr0.00511933
X-RAY DIFFRACTIONf_dihedral_angle_d11.19164075
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.690.39130.359715039X-RAY DIFFRACTION94.19
5.46-6.250.29631470.22723099X-RAY DIFFRACTION97.42

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