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- PDB-7ucl: SxtA Methyltransferase variant F458H in complex with Mn2+ and malonate -

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Basic information

Entry
Database: PDB / ID: 7ucl
TitleSxtA Methyltransferase variant F458H in complex with Mn2+ and malonate
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
MALONATE ION / : / Polyketide synthase-related protein
Similarity search - Component
Biological speciesCylindrospermopsis raciborskii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.09 Å
AuthorsLao, Y. / 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)162,6706
Polymers162,3562
Non-polymers3144
Water4,324240
1
A: Polyketide synthase-related protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,3353
Polymers81,1781
Non-polymers1572
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Polyketide synthase-related protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,3353
Polymers81,1781
Non-polymers1572
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)78.640, 83.794, 117.821
Angle α, β, γ (deg.)90.000, 103.090, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein Polyketide synthase-related protein


Mass: 81177.984 Da / Num. of mol.: 2 / Mutation: F458H
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-MLI / MALONATE ION


Mass: 102.046 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H2O4 / 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 240 / 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: 2.33 Å3/Da / Density % sol: 47.18 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 12-14 mg/mL SxtA methyltransferase F458H in (5mM S-adenosyl-L-methionine (SAM), 2mM sodium malonate, 5mM (R)-pantetheine, 5mM MnCl2) Well solution: 18% PEG 33550, 0.16M LiSO4, 0.1M Tris pH7

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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: Aug 6, 2020
RadiationMonochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 2.09→47.34 Å / Num. obs: 86845 / % possible obs: 98.28 % / Redundancy: 6.9 % / Biso Wilson estimate: 46.48 Å2 / CC1/2: 0.997 / CC star: 0.999 / Rmerge(I) obs: 0.1054 / Rpim(I) all: 0.04329 / Rrim(I) all: 0.1142 / Net I/σ(I): 10.9
Reflection shellResolution: 2.09→2.16 Å / Redundancy: 6.6 % / Rmerge(I) obs: 1.355 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 54134 / CC1/2: 0.756 / CC star: 0.928 / % possible all: 92.74

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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: 7UCI

7uci


Resolution: 2.09→47.34 Å / SU ML: 0.3163 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.0616
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.2392 2000 2.3 %random selection
Rwork0.2061 165761 --
obs0.2069 86787 97.7 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 52.29 Å2
Refinement stepCycle: LAST / Resolution: 2.09→47.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9832 0 16 240 10088
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008910061
X-RAY DIFFRACTIONf_angle_d1.023113643
X-RAY DIFFRACTIONf_chiral_restr0.05451542
X-RAY DIFFRACTIONf_plane_restr0.01111759
X-RAY DIFFRACTIONf_dihedral_angle_d14.86833735
LS refinement shellResolution: 2.09→2.17 Å
RfactorNum. reflection% reflection
Rfree0.3485 187 -
Rwork0.3275 8133 -
obs--92.74 %

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