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- PDB-8rxg: Crystal structure of alpha-keto C-methyl transferase SgvM bound to SAM -

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Basic information

Entry
Database: PDB / ID: 8rxg
TitleCrystal structure of alpha-keto C-methyl transferase SgvM bound to SAM
ComponentsMethyltransferase
KeywordsTRANSFERASE / S adenosylmethionine-dependent methyltransferases / biocatalysis / C-alkylation
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-ADENOSYLMETHIONINE / Methyltransferase
Similarity search - Component
Biological speciesStreptomyces griseoviridis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.813 Å
AuthorsGerhardt, S. / Andexer, J.N.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Chembiochem / Year: 2024
Title: Structures and Protein Engineering of the alpha-Keto Acid C-Methyltransferases SgvM and MrsA for Rational Substrate Transfer.
Authors: Sommer-Kamann, C. / Breiltgens, J. / Zou, Z. / Gerhardt, S. / Saleem-Batcha, R. / Kemper, F. / Einsle, O. / Andexer, J.N. / Muller, M.
History
DepositionFeb 7, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 24, 2024Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2024Group: Database references / Structure summary / Category: citation / pdbx_entry_details
Item: _citation.journal_volume / _pdbx_entry_details.has_protein_modification

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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)37,5415
Polymers36,9111
Non-polymers6294
Water6,269348
1
A: Methyltransferase
hetero molecules

A: Methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,08210
Polymers73,8232
Non-polymers1,2598
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area8050 Å2
ΔGint-130 kcal/mol
Surface area25980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.205, 67.205, 183.006
Angle α, β, γ (deg.)90, 90, 90
Int Tables number96
Space group name H-MP43212

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Components

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Protein , 1 types, 1 molecules A

#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) / Plasmid: pET28a (+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-Gold (DE3) / References: UniProt: R9UTR3

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Non-polymers , 5 types, 352 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: 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
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-SAM / S-ADENOSYLMETHIONINE


Mass: 398.437 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H22N6O5S
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 348 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationN

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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: 2.8 Å3/Da / Density % sol: 56.06 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 100 mM Tris/HCl pH 8.5, 250 mM Li2SO4, and 23% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1.00004 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 13, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00004 Å / Relative weight: 1
ReflectionResolution: 1.813→63.0857 Å / Num. obs: 39049 / % possible obs: 100 % / Redundancy: 26.3 % / CC1/2: 0.999 / Rmerge(I) obs: 0.203 / Rpim(I) all: 0.059 / Rsym value: 0.203 / Net I/σ(I): 12.6
Reflection shellResolution: 1.813→1.844 Å / Redundancy: 27.5 % / Rmerge(I) obs: 8.708 / Mean I/σ(I) obs: 0.5 / Num. unique obs: 1880 / CC1/2: 0.35 / Rsym value: 8.708 / % possible all: 100

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Processing

Software
NameVersionClassification
BUSTER2.10.4refinement
autoPROCdata reduction
XDSJun 30, 2023data reduction
autoPROC1.0.5data scaling
Aimless0.7.15data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.813→63.09 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.926 / SU R Cruickshank DPI: 0.15 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.13 / SU Rfree Blow DPI: 0.127 / SU Rfree Cruickshank DPI: 0.12
RfactorNum. reflection% reflectionSelection details
Rfree0.2371 1927 -RANDOM
Rwork0.1946 ---
obs0.1966 38503 98.6 %-
Displacement parametersBiso mean: 53.89 Å2
Baniso -1Baniso -2Baniso -3
1--3.8479 Å20 Å20 Å2
2---3.8479 Å20 Å2
3---7.6958 Å2
Refine analyzeLuzzati coordinate error obs: 0.23 Å
Refinement stepCycle: LAST / Resolution: 1.813→63.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2571 0 38 348 2957
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.015207HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.959368HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1563SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes874HARMONIC5
X-RAY DIFFRACTIONt_it5207HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion346SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies1HARMONIC1
X-RAY DIFFRACTIONt_ideal_dist_contact4901SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion3.5
X-RAY DIFFRACTIONt_other_torsion15.7
LS refinement shellResolution: 1.813→1.83 Å
RfactorNum. reflection% reflection
Rfree0.3693 42 -
Rwork0.3844 --
obs--80.82 %
Refinement TLS params.Origin x: -0.4658 Å / Origin y: 23.2931 Å / Origin z: -3.5484 Å
111213212223313233
T-0.0202 Å20.0304 Å2-0.0111 Å2-0.1103 Å20.0091 Å2--0.0882 Å2
L0.7328 °20.2 °2-0.215 °2-0.8995 °2-0.119 °2--1.6725 °2
S0.0232 Å °0.0114 Å °-0.1268 Å °0.0114 Å °0.0137 Å °-0.4513 Å °-0.1268 Å °-0.4513 Å °-0.0368 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A4 - 339
2X-RAY DIFFRACTION1{ A|* }A1001 - 1005

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