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- PDB-8ftr: SgvM methyltransferase with MTA and alpha-ketoleucine -

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Basic information

Entry
Database: PDB / ID: 8ftr
TitleSgvM methyltransferase with MTA and alpha-ketoleucine
ComponentsMethyltransferase
KeywordsBIOSYNTHETIC PROTEIN / Methyltransferase
Function / homology
Function and homology information


methyltransferase activity / methylation / metal ion binding
Similarity search - Function
Methyltransferase type 12 / Methyltransferase domain / O-methyltransferase COMT-type / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / S-adenosyl-L-methionine-dependent methyltransferase superfamily
Similarity search - Domain/homology
2-OXO-4-METHYLPENTANOIC ACID / 5'-DEOXY-5'-METHYLTHIOADENOSINE / Methyltransferase
Similarity search - Component
Biological speciesStreptomyces griseoviridis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.13 Å
AuthorsKuzelka, K. / Nair, S.K.
Funding support1items
OrganizationGrant numberCountry
Other private
CitationJournal: Nat Commun / Year: 2023
Title: A biocatalytic platform for asymmetric alkylation of alpha-keto acids by mining and engineering of methyltransferases.
Authors: Ju, S. / Kuzelka, K.P. / Guo, R. / Krohn-Hansen, B. / Wu, J. / Nair, S.K. / Yang, Y.
History
DepositionJan 13, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 1, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,4044
Polymers36,9111
Non-polymers4933
Water2,216123
1
A: Methyltransferase
hetero molecules

A: Methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,8098
Polymers73,8232
Non-polymers9866
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
Buried area8620 Å2
ΔGint-115 kcal/mol
Surface area26160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.134, 67.134, 184.338
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Methyltransferase /


Mass: 36911.477 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces griseoviridis (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: R9UTR3
#2: Chemical ChemComp-MTA / 5'-DEOXY-5'-METHYLTHIOADENOSINE / 5′-Methylthioadenosine


Mass: 297.334 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H15N5O3S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-COI / 2-OXO-4-METHYLPENTANOIC ACID / alpha-ketoisocaproic acid / Alpha-Ketoisocaproic acid


Mass: 130.142 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H10O3 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 123 / 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: 2.81 Å3/Da / Density % sol: 56.28 %
Crystal growTemperature: 283 K / Method: vapor diffusion / Details: PEG 3350 pH 7.5-8.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97856 Å
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Aug 2, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 2.129→54.3 Å / Num. obs: 23766 / % possible obs: 96.8 % / Redundancy: 19.5 % / CC1/2: 1 / Rmerge(I) obs: 0.098 / Net I/σ(I): 23.3
Reflection shellResolution: 2.129→2.136 Å / Num. unique obs: 4532 / CC1/2: 0.753

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Processing

Software
NameVersionClassification
REFMAC5refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 2.13→54.27 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.37 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2456 1183 4.98 %
Rwork0.2106 --
obs0.2124 23758 96.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.13→54.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2554 0 30 123 2707
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092638
X-RAY DIFFRACTIONf_angle_d1.0033590
X-RAY DIFFRACTIONf_dihedral_angle_d16.308380
X-RAY DIFFRACTIONf_chiral_restr0.064398
X-RAY DIFFRACTIONf_plane_restr0.007479
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.13-2.230.30371340.27312860X-RAY DIFFRACTION100
2.23-2.340.2741560.24712848X-RAY DIFFRACTION100
2.34-2.490.27721640.23422853X-RAY DIFFRACTION100
2.49-2.650.30791340.22642481X-RAY DIFFRACTION100
2.7-2.950.29671460.23642685X-RAY DIFFRACTION100
2.95-3.380.31371410.24442927X-RAY DIFFRACTION100
3.38-4.260.22781630.19652784X-RAY DIFFRACTION95
4.26-54.270.1891450.1813137X-RAY DIFFRACTION99

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