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

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Basic information

Entry
Database: PDB / ID: 8rvc
TitleCrystal structure of alpha keto acid C-methyl-transferases MrsA bound to ketoarginine
Components2-ketoarginine methyltransferase
KeywordsTRANSFERASE / S adenosylmethionine-dependent methyltransferases / biocatalysis / C-alkylation / asymmetric methylation / mutagenesis
Function / homology
Function and homology information


5-guanidino-2-oxopentanoate (3R)-methyltransferase / S-adenosylmethionine-dependent methyltransferase activity / antibiotic biosynthetic process / methylation
Similarity search - Function
2-ketoarginine methyltransferase / S-adenosyl-L-methionine-dependent methyltransferase superfamily
Similarity search - Domain/homology
5-[(diaminomethylidene)amino]-2-oxopentanoic acid / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / 2-ketoarginine methyltransferase
Similarity search - Component
Biological speciesPseudomonas syringae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.969 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
DepositionFeb 1, 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: 2-ketoarginine methyltransferase
B: 2-ketoarginine methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,18620
Polymers81,8892
Non-polymers1,29618
Water6,684371
1
A: 2-ketoarginine methyltransferase
hetero molecules

A: 2-ketoarginine methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,10720
Polymers81,8892
Non-polymers1,21818
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_575-x,-y+2,z1
Buried area9380 Å2
ΔGint-146 kcal/mol
Surface area27030 Å2
MethodPISA
2
B: 2-ketoarginine methyltransferase
hetero molecules

B: 2-ketoarginine methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,26420
Polymers81,8892
Non-polymers1,37518
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_575-x,-y+2,z1
Buried area9160 Å2
ΔGint-107 kcal/mol
Surface area27220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)148.45, 65.873, 75.041
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: 40944.586 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) / Strain (production host): BL21-Gold (DE3)
References: UniProt: D5FKJ3, 5-guanidino-2-oxopentanoate (3R)-methyltransferase

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Non-polymers , 7 types, 389 molecules

#2: Chemical ChemComp-NWG / 5-[(diaminomethylidene)amino]-2-oxopentanoic acid


Mass: 173.170 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H11N3O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#6: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#7: Chemical
ChemComp-NA / SODIUM ION


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


Mass: 18.015 Da / Num. of mol.: 371 / 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: 2.24 Å3/Da / Density % sol: 45.1 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 100mM HEPES, 300mM potassium chloride, 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 2M / Detector: PIXEL / Date: Jul 1, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.97→49.51 Å / Num. obs: 51937 / % possible obs: 98 % / Redundancy: 12.6 % / CC1/2: 0.998 / Rmerge(I) obs: 0.148 / Rpim(I) all: 0.043 / Rrim(I) all: 0.154 / Net I/σ(I): 14
Reflection shellResolution: 1.97→2.02 Å / Redundancy: 9.1 % / Rmerge(I) obs: 0.978 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 2612 / CC1/2: 0.755 / Rpim(I) all: 0.318 / Rrim(I) all: 1.033 / % possible all: 71.7

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Processing

Software
NameVersionClassification
BUSTER2.10.4refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.969→49.51 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.927 / SU R Cruickshank DPI: 0.336 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.179 / SU Rfree Blow DPI: 0.147 / SU Rfree Cruickshank DPI: 0.145
RfactorNum. reflection% reflectionSelection details
Rfree0.2197 2596 -RANDOM
Rwork0.1946 ---
obs0.1959 51885 98 %-
Displacement parametersBiso mean: 31.36 Å2
Baniso -1Baniso -2Baniso -3
1--2.1521 Å20 Å20 Å2
2---4.4895 Å20 Å2
3---6.6416 Å2
Refine analyzeLuzzati coordinate error obs: 0.23 Å
Refinement stepCycle: LAST / Resolution: 1.969→49.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5306 0 82 371 5759
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.00810816HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.9119494HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d3231SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes1757HARMONIC5
X-RAY DIFFRACTIONt_it5521HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion698SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact8641SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion2.88
X-RAY DIFFRACTIONt_other_torsion15.09
LS refinement shellResolution: 1.97→2 Å
RfactorNum. reflection% reflection
Rfree0.3491 52 -
Rwork0.2964 --
obs0.2989 1038 50.36 %
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)
10.40370.15120.02640.3094-0.09060.5797-0.06250.0148-0.10890.01480.02050.1043-0.10890.10430.04190.0134-0.0134-0.0168-0.0442-0.0044-0.034812.616178.875639.226
20.4121-0.1058-0.05250.1756-0.07130.278-0.0124-0.02590.0163-0.0259-0.0020.05730.01630.05730.0144-0.05140.02860.00160.01730.0026-0.012815.93657.2822.8195
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ B|* }B31 - 370
2X-RAY DIFFRACTION1{ B|* }B1002 - 1001
3X-RAY DIFFRACTION2{ A|* }A31 - 370
4X-RAY DIFFRACTION2{ A|* }A1001 - 1006

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