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- PDB-8rww: Crystal structure of native alpha-keto C-methyl transferase SgvM ... -

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Basic information

Entry
Database: PDB / ID: 8rww
TitleCrystal structure of native 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 / MOLECULAR REPLACEMENT / Resolution: 1.95 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 5, 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)37,1424
Polymers36,9111
Non-polymers2313
Water5,981332
1
A: Methyltransferase
hetero molecules

A: Methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,2858
Polymers73,8232
Non-polymers4626
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area8000 Å2
ΔGint-124 kcal/mol
Surface area26580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.278, 67.278, 182.967
Angle α, β, γ (deg.)90, 90, 90
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) / Plasmid: pET28a (+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-Gold (DE3) / References: UniProt: R9UTR3
#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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 332 / Source method: isolated from a natural source / Formula: H2O
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: 56.14 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 20% PEG 3350, 250 mM Li2SO4, and 100 mM Tris/HCl pH 8.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 18, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.95→20.09 Å / Num. obs: 31639 / % possible obs: 99.9 % / Redundancy: 25.8 % / CC1/2: 0.999 / Rmerge(I) obs: 0.252 / Rpim(I) all: 0.05 / Rrim(I) all: 0.257 / Net I/σ(I): 13.4
Reflection shellResolution: 1.95→2 Å / Num. unique obs: 2168 / CC1/2: 0.463

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Processing

Software
NameVersionClassification
BUSTER2.10.4refinement
autoPROCdata reduction
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.95→20.09 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.947 / SU R Cruickshank DPI: 0.195 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.152 / SU Rfree Blow DPI: 0.134 / SU Rfree Cruickshank DPI: 0.126
RfactorNum. reflection% reflectionSelection details
Rfree0.2123 1598 -RANDOM
Rwork0.1822 ---
obs0.1837 31509 99.8 %-
Displacement parametersBiso mean: 49.52 Å2
Baniso -1Baniso -2Baniso -3
1--4.1748 Å20 Å20 Å2
2---4.1748 Å20 Å2
3---8.3496 Å2
Refine analyzeLuzzati coordinate error obs: 0.25 Å
Refinement stepCycle: LAST / Resolution: 1.95→20.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2557 0 11 332 2900
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.015181HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.979331HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1557SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes869HARMONIC5
X-RAY DIFFRACTIONt_it5181HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion343SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies4HARMONIC1
X-RAY DIFFRACTIONt_ideal_dist_contact4823SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion3.35
X-RAY DIFFRACTIONt_other_torsion14.26
LS refinement shellResolution: 1.95→1.96 Å
RfactorNum. reflection% reflection
Rfree0.371 44 -
Rwork0.3096 --
obs0.3141 631 100 %
Refinement TLS params.Origin x: -0.6478 Å / Origin y: 23.3564 Å / Origin z: -3.4121 Å
111213212223313233
T-0.0301 Å20.0402 Å2-0.0048 Å2-0.1053 Å20.0118 Å2--0.0954 Å2
L0.8175 °20.2182 °2-0.1703 °2-0.9808 °2-0.1173 °2--1.6692 °2
S0.0271 Å °0.011 Å °-0.1326 Å °0.011 Å °0.0152 Å °-0.4331 Å °-0.1326 Å °-0.4331 Å °-0.0423 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A6 - 339
2X-RAY DIFFRACTION1{ A|* }A1001 - 1003

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