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- PDB-8rxf: Crystal structure of S-SAD phased alpha-keto C-methyl transferase... -

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Basic information

Entry
Database: PDB / ID: 8rxf
TitleCrystal structure of S-SAD phased alpha-keto C-methyl transferase SgvM bound to ketoleucine
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 / Methyltransferase
Similarity search - Component
Biological speciesStreptomyces griseoviridis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.27 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 3, 2024Provider: repository / Type: Initial release
Revision 1.1Jul 24, 2024Group: Database references / Category: citation / citation_author / Item: _citation.title / _citation_author.identifier_ORCID
Revision 1.2Oct 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)37,2355
Polymers36,9111
Non-polymers3234
Water3,783210
1
A: Methyltransferase
hetero molecules

A: Methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,46910
Polymers73,8232
Non-polymers6468
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area8430 Å2
ΔGint-120 kcal/mol
Surface area26540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.054, 67.054, 183.074
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) / Production host: Escherichia coli (E. coli) / References: UniProt: R9UTR3

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Non-polymers , 5 types, 214 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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 210 / 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: 2.05 Å3/Da / Density % sol: 40.09 %
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: 2.07505 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 1, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 2.07505 Å / Relative weight: 1
ReflectionResolution: 2.27→91.54 Å / Num. obs: 20302 / % possible obs: 99.9 % / Redundancy: 171.5 % / CC1/2: 1 / Rmerge(I) obs: 0.129 / Rpim(I) all: 0.01 / Rrim(I) all: 0.129 / Net I/σ(I): 50.6
Reflection shellResolution: 2.27→2.39 Å / Rmerge(I) obs: 1.534 / Mean I/σ(I) obs: 3.1 / Num. unique obs: 2883 / CC1/2: 0.913 / Rpim(I) all: 0.181 / Rrim(I) all: 1.546

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Processing

Software
NameVersionClassification
BUSTER2.10.4refinement
autoPROCdata reduction
autoPROCdata scaling
HKL2Mapphasing
RefinementMethod to determine structure: SAD / Resolution: 2.27→62.96 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.91 / SU R Cruickshank DPI: 0.236 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.266 / SU Rfree Blow DPI: 0.2 / SU Rfree Cruickshank DPI: 0.192
RfactorNum. reflection% reflectionSelection details
Rfree0.2286 966 -RANDOM
Rwork0.1869 ---
obs0.189 20228 100 %-
Displacement parametersBiso mean: 62.15 Å2
Baniso -1Baniso -2Baniso -3
1--6.9646 Å20 Å20 Å2
2---6.9646 Å20 Å2
3---13.9292 Å2
Refine analyzeLuzzati coordinate error obs: 0.25 Å
Refinement stepCycle: LAST / Resolution: 2.27→62.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2566 0 17 210 2793
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0072642HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.833593HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d897SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes469HARMONIC5
X-RAY DIFFRACTIONt_it2642HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion340SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact2273SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion2.91
X-RAY DIFFRACTIONt_other_torsion16.87
LS refinement shellResolution: 2.27→2.28 Å
RfactorNum. reflection% reflection
Rfree0.3321 21 -
Rwork0.2951 --
obs0.2969 422 98.09 %
Refinement TLS params.Origin x: 34.0033 Å / Origin y: 10.004 Å / Origin z: -3.2656 Å
111213212223313233
T-0.065 Å20.0459 Å2-0.0128 Å2-0.078 Å2-0.0301 Å2--0.0444 Å2
L0.7725 °20.3574 °20.205 °2-1.2617 °20.2581 °2--1.836 °2
S0.0099 Å °0.0546 Å °0.1464 Å °0.0546 Å °0.0738 Å °0.4268 Å °0.1464 Å °0.4268 Å °-0.0837 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A5 - 339
2X-RAY DIFFRACTION1{ A|* }A501 - 505

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