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- PDB-8rwm: Crystal structure of selenomethionine derivatized alpha keto acid... -

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Basic information

Entry
Database: PDB / ID: 8rwm
TitleCrystal structure of selenomethionine derivatized alpha keto acid C-methyl-transferases MrsA
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 / 2-ketoarginine methyltransferase
Function and homology information
Biological speciesPseudomonas syringae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.644 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 / pdbx_modification_feature
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: 2-ketoarginine methyltransferase
B: 2-ketoarginine methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,2056
Polymers78,1092
Non-polymers964
Water18,0331001
1
A: 2-ketoarginine methyltransferase
hetero molecules

A: 2-ketoarginine methyltransferase
hetero molecules

B: 2-ketoarginine methyltransferase
hetero molecules

B: 2-ketoarginine methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)156,41012
Polymers156,2184
Non-polymers1928
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
crystal symmetry operation1_554x,y,z-11
crystal symmetry operation2_654-x+1,-y,z-11
Buried area18460 Å2
ΔGint-219 kcal/mol
Surface area49420 Å2
Unit cell
Length a, b, c (Å)147.847, 65.531, 74.823
Angle α, β, γ (deg.)90, 90, 90
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein 2-ketoarginine methyltransferase


Mass: 39054.605 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
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1001 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.34 Å3/Da / Density % sol: 47.37 %
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: X06DA / Wavelength: 0.97943 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 15, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97943 Å / Relative weight: 1
ReflectionResolution: 1.64→74.82 Å / Num. obs: 89187 / % possible obs: 100 % / Redundancy: 48.7 % / CC1/2: 1 / Rmerge(I) obs: 0.164 / Rpim(I) all: 0.023 / Rrim(I) all: 0.166 / Net I/σ(I): 25.6
Reflection shellResolution: 1.64→1.73 Å / Redundancy: 29 % / Num. unique obs: 12888 / CC1/2: 0.777 / Rpim(I) all: 0.332 / % possible all: 100

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Processing

Software
NameVersionClassification
BUSTER2.10.4refinement
autoPROCdata reduction
autoPROCdata scaling
HKL2Mapphasing
RefinementMethod to determine structure: SAD / Resolution: 1.644→74.82 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.958 / SU R Cruickshank DPI: 0.101 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.092 / SU Rfree Blow DPI: 0.085 / SU Rfree Cruickshank DPI: 0.08
RfactorNum. reflection% reflectionSelection details
Rfree0.1825 4467 -RANDOM
Rwork0.1595 ---
obs0.1607 89019 99.9 %-
Displacement parametersBiso mean: 26.6 Å2
Baniso -1Baniso -2Baniso -3
1-0.3316 Å20 Å20 Å2
2---2.791 Å20 Å2
3---2.4594 Å2
Refine analyzeLuzzati coordinate error obs: 0.18 Å
Refinement stepCycle: LAST / Resolution: 1.644→74.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5316 0 4 1001 6321
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0110692HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.0119318HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d3161SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes1727HARMONIC5
X-RAY DIFFRACTIONt_it10692HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion695SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies1HARMONIC1
X-RAY DIFFRACTIONt_ideal_dist_contact10493SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion3.88
X-RAY DIFFRACTIONt_other_torsion15.03
LS refinement shellResolution: 1.644→1.66 Å
RfactorNum. reflection% reflection
Rfree0.3329 95 -
Rwork0.2655 --
obs--99.25 %
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)
10.6089-0.0729-0.03840.40420.14410.5718-0.06270.00190.11550.0019-0.0084-0.07510.1155-0.07510.07110.0048-0.01240.0224-0.0152-0.010.002161.1691-12.746139.2164
20.2387-0.0482-0.080.22970.10480.3241-0.02330.0073-0.00810.00730.0073-0.0324-0.0081-0.03240.016-0.020.0294-0.00770.02320.0013-0.01958.10598.47832.9412
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ B|* }B30 - 370
2X-RAY DIFFRACTION1{ B|* }B1002 - 1004
3X-RAY DIFFRACTION2{ A|* }A30 - 370
4X-RAY DIFFRACTION2{ A|* }A1001

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