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- PDB-8r4z: Crystal structure of alpha keto acid C-methyl-transferases MrsA n... -

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Basic information

Entry
Database: PDB / ID: 8r4z
TitleCrystal structure of alpha keto acid C-methyl-transferases MrsA native-form
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 / MOLECULAR REPLACEMENT / Resolution: 1.54 Å
AuthorsGerhardt, S. / Kemper, F. / 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
DepositionNov 15, 2023Deposition 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: 2-ketoarginine methyltransferase
B: 2-ketoarginine methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,6446
Polymers77,5462
Non-polymers974
Water14,520806
1
A: 2-ketoarginine methyltransferase
hetero molecules

A: 2-ketoarginine methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,6446
Polymers77,5462
Non-polymers974
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
Buried area7370 Å2
ΔGint-96 kcal/mol
Surface area26360 Å2
2
B: 2-ketoarginine methyltransferase
hetero molecules

B: 2-ketoarginine methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,6446
Polymers77,5462
Non-polymers974
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
Buried area7390 Å2
ΔGint-97 kcal/mol
Surface area26810 Å2
Unit cell
Length a, b, c (Å)148.135, 66.173, 74.312
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#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 / Production host: Escherichia coli (E. coli) / References: UniProt: D5FKJ3
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 806 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.35 Å3/Da / Density % sol: 47.62 %
Crystal growTemperature: 273 K / Method: vapor diffusion, sitting drop / 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 / Detector: PIXEL / Date: Apr 19, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.538→74.31 Å / Num. obs: 109165 / % possible obs: 100 % / Redundancy: 12.7 % / CC1/2: 0.99 / Rmerge(I) obs: 0.1 / Rpim(I) all: 0.029 / Rsym value: 0.1 / Net I/σ(I): 15.2
Reflection shellResolution: 1.538→1.62 Å / Redundancy: 13 % / Num. unique obs: 15766 / CC1/2: 0.85 / % possible all: 99.4

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Processing

Software
NameVersionClassification
autoPROCdata reduction
Aimlessdata scaling
MOLREPphasing
BUSTER2.10.1refinement
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: IN-HOUSE SAD STRUCTURE

Resolution: 1.54→74.31 Å / Cor.coef. Fo:Fc: 0.9556 / Cor.coef. Fo:Fc free: 0.9495 / SU R Cruickshank DPI: 0.069 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.073 / SU Rfree Blow DPI: 0.071 / SU Rfree Cruickshank DPI: 0.068
RfactorNum. reflection% reflectionSelection details
Rfree0.1866 5311 4.89 %RANDOM
Rwork0.1665 ---
obs0.1675 108582 99.93 %-
Displacement parametersBiso mean: 26.64 Å2
Baniso -1Baniso -2Baniso -3
1--1.2392 Å20 Å20 Å2
2---5.3123 Å20 Å2
3---6.5515 Å2
Refine analyzeLuzzati coordinate error obs: 0.172 Å
Refinement stepCycle: LAST / Resolution: 1.54→74.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5342 0 4 806 6152
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.015466HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.997412HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1878SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes135HARMONIC2
X-RAY DIFFRACTIONt_gen_planes808HARMONIC5
X-RAY DIFFRACTIONt_it5466HARMONIC20
X-RAY DIFFRACTIONt_nbd2SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion3.51
X-RAY DIFFRACTIONt_other_torsion15.59
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion698SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact7133SEMIHARMONIC4
LS refinement shellResolution: 1.54→1.58 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2133 368 4.61 %
Rwork0.2022 7608 -
all0.2028 7976 -
obs--99.93 %
Refinement TLS params.

Method: refined / 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)
10.2202-0.07010.05450.2885-0.08940.4269-0.0392-0.0084-0.02210.02660.0073-0.04080.03910.0640.032-0.04140.01450.009-0.0272-0.0008-0.021715.705324.45472.7292
20.26040.0016-0.17520.3969-0.15710.6359-0.0036-0.02190.0606-0.0385-0.0235-0.0616-0.11160.10290.0271-0.0309-0.0318-0.0106-0.057-0.0007-0.037113.090245.43538.5716
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }

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