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- PDB-8fts: SgvM methyltransferase with SAH and alpha-ketoleucine -

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Basic information

Entry
Database: PDB / ID: 8fts
TitleSgvM methyltransferase with SAH 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 / 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 / S-ADENOSYL-L-HOMOCYSTEINE / Methyltransferase
Similarity search - Component
Biological speciesStreptomyces griseoviridis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 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

Downloads & links

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Assembly

Deposited unit
A: Methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,4914
Polymers36,9111
Non-polymers5803
Water1,62190
1
A: Methyltransferase
hetero molecules

A: Methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,9838
Polymers73,8232
Non-polymers1,1606
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
Buried area7590 Å2
ΔGint-113 kcal/mol
Surface area25190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.347, 68.347, 186.207
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-690-

HOH

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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-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H20N6O5S / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-COI / 2-OXO-4-METHYLPENTANOIC 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


Mass: 18.015 Da / Num. of mol.: 90 / 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: 2.95 Å3/Da / Density % sol: 58.24 %
Crystal growTemperature: 283 K / Method: vapor diffusion / Details: PEG 3350 pH 7.5

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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: Nov 20, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 2.2→38.133 Å / Num. obs: 23134 / % possible obs: 99.4 % / Redundancy: 21.7 % / CC1/2: 0.999 / Rmerge(I) obs: 0.113 / Net I/σ(I): 15.8
Reflection shellResolution: 2.2→2.207 Å / Rmerge(I) obs: 1.823 / Num. unique obs: 5110 / CC1/2: 0.792

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Processing

Software
NameVersionClassification
REFMAC5refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→25 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.942 / SU B: 6.65 / SU ML: 0.163 / Cross valid method: THROUGHOUT / ESU R: 0.23 / ESU R Free: 0.192 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.2459 1142 4.9 %RANDOM
Rwork0.2111 ---
obs0.21282 21977 99.26 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 62.487 Å2
Baniso -1Baniso -2Baniso -3
1-0.66 Å2-0 Å2-0 Å2
2--0.66 Å2-0 Å2
3----1.32 Å2
Refinement stepCycle: 1 / Resolution: 2.2→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2546 0 36 90 2672
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0122636
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1551.6363588
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3335332
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.34720.191157
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.93115388
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.4661529
X-RAY DIFFRACTIONr_chiral_restr0.1090.2342
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022077
X-RAY DIFFRACTIONr_gen_planes_other
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_it3.2896.1481334
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it5.0339.2051664
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.9136.3421302
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined8.39181.6323725
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.346 88 -
Rwork0.308 1563 -
obs--100 %

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