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- PDB-8rvs: Crystal structure of alpha keto acid C-methyl-transferases MrsA b... -

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Basic information

Entry
Database: PDB / ID: 8rvs
TitleCrystal structure of alpha keto acid C-methyl-transferases MrsA bound to SAM
Components2-ketoarginine methyltransferase
KeywordsTRANSFERASE / S adenosylmethionine-dependent methyltransferases / biocatalysis / C-alkylation / asymmetric methylation / mutagenesis
Function / homology5-guanidino-2-oxopentanoate (3R)-methyltransferase / 2-ketoarginine methyltransferase / S-adenosylmethionine-dependent methyltransferase activity / antibiotic biosynthetic process / methylation / S-adenosyl-L-methionine-dependent methyltransferase superfamily / DI(HYDROXYETHYL)ETHER / S-ADENOSYLMETHIONINE / 2-ketoarginine methyltransferase
Function and homology information
Biological speciesPseudomonas syringae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.632 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 2, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 3, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 2-ketoarginine methyltransferase
B: 2-ketoarginine methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,75813
Polymers77,5462
Non-polymers1,21211
Water12,953719
1
B: 2-ketoarginine methyltransferase
hetero molecules

B: 2-ketoarginine methyltransferase
hetero molecules

A: 2-ketoarginine methyltransferase
hetero molecules

A: 2-ketoarginine methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)157,51626
Polymers155,0934
Non-polymers2,42422
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_765-x+2,-y+1,z1
crystal symmetry operation1_556x,y,z+11
crystal symmetry operation2_766-x+2,-y+1,z+11
Buried area19830 Å2
ΔGint-267 kcal/mol
Surface area47110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)147.246, 65.68, 74.58
Angle α, β, γ (deg.)90, 90, 90
Int Tables number18
Space group name H-MP21212

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein 2-ketoarginine methyltransferase


Mass: 38773.242 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas syringae (bacteria) / Gene: mrsA / Plasmid: pET-28b (+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-Gold (DE3) / References: UniProt: D5FKJ3

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Non-polymers , 6 types, 730 molecules

#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-SAM / S-ADENOSYLMETHIONINE


Mass: 398.437 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H22N6O5S / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#6: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 719 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.33 Å3/Da / Density % sol: 47.1 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 100 mM HEPES pH 7.5, 300 mM NaCl, 28% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jun 14, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.632→66.533 Å / Num. obs: 90343 / % possible obs: 99.7 % / Redundancy: 4.4 % / CC1/2: 0.997 / Rmerge(I) obs: 0.099 / Rpim(I) all: 0.053 / Rrim(I) all: 0.113 / Net I/σ(I): 8.5
Reflection shellResolution: 1.632→1.66 Å / Redundancy: 4.5 % / Rmerge(I) obs: 1.574 / Num. unique obs: 4489 / CC1/2: 0.389 / Rpim(I) all: 0.837 / % possible all: 99.9

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Processing

Software
NameVersionClassification
BUSTER2.10.4refinement
autoPROCdata reduction
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.632→66.53 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.952 / SU R Cruickshank DPI: 0.091 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.098 / SU Rfree Blow DPI: 0.093 / SU Rfree Cruickshank DPI: 0.09
RfactorNum. reflection% reflectionSelection details
Rfree0.2104 4518 -RANDOM
Rwork0.1833 ---
obs0.1846 90041 99.4 %-
Displacement parametersBiso mean: 28.17 Å2
Baniso -1Baniso -2Baniso -3
1--0.958 Å20 Å20 Å2
2---4.0357 Å20 Å2
3---4.9937 Å2
Refine analyzeLuzzati coordinate error obs: 0.21 Å
Refinement stepCycle: LAST / Resolution: 1.632→66.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5316 0 78 719 6113
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.015527HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.917490HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1901SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes951HARMONIC5
X-RAY DIFFRACTIONt_it5527HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion707SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact5714SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion3.44
X-RAY DIFFRACTIONt_other_torsion15.22
LS refinement shellResolution: 1.64→1.66 Å
RfactorNum. reflection% reflection
Rfree0.3202 84 -
obs--96.08 %
Refinement TLS params.

Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.13530.0212-0.02810.1137-0.07510.2436-0.0467-0.0820.1096-0.0820.0270.02550.10960.02550.01970.0877-0.04740.03440.076-0.0072-0.0163159.90820.1533-1.7308
20.12990.0088-0.09740.0702-0.1010.3749-0.03810.0621-0.10470.06210.00270.1445-0.10470.14450.03540.08040.021-0.02780.0618-0.0084-0.0199163.14341.113734.4308
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ B|* }B30 - 370
2X-RAY DIFFRACTION1{ B|* }B1001 - 1003
3X-RAY DIFFRACTION2{ A|* }A30 - 370
4X-RAY DIFFRACTION2{ A|* }A1001 - 1003

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