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- PDB-8rpr: Crystal Structure of SgvM methyltransferase in complex with alpha... -

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Basic information

Entry
Database: PDB / ID: 8rpr
TitleCrystal Structure of SgvM methyltransferase in complex with alpha-ketoleucine and Zn2+ ion
ComponentsMethyltransferase
KeywordsTRANSFERASE / complex / Methylransferase
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: 2.14 Å
AuthorsSaleem-Batcha, R. / Zou, Z. / Breiltgens, J. / Mueller, M. / Andexer, J.N.
Funding support Germany, European Union, 2items
OrganizationGrant numberCountry
German Research Foundation (DFG)235777276/RTG1976 Germany
European Research Council (ERC)ERC project 716966European Union
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
DepositionJan 16, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 24, 2024Provider: repository / Type: Initial release
Revision 1.1Oct 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

Downloads & links

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Assembly

Deposited unit
A: Methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,2649
Polymers36,9111
Non-polymers3538
Water1,964109
1
A: Methyltransferase
hetero molecules

A: Methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,52818
Polymers73,8232
Non-polymers70516
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area9700 Å2
ΔGint-219 kcal/mol
Surface area26230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.031, 67.031, 182.745
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Space group name HallP4nw2abw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+3/4
#3: y+1/2,-x+1/2,z+1/4
#4: x+1/2,-y+1/2,-z+1/4
#5: -x+1/2,y+1/2,-z+3/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2

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Components

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Protein , 1 types, 1 molecules A

#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) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: R9UTR3

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Non-polymers , 5 types, 117 molecules

#2: 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
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 109 / 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: 2.78 Å3/Da / Density % sol: 55.77 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop
Details: 100 mM Tris/HCl pH 8.5, 250 mM Li2SO4, and 23% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.2802 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Sep 4, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2802 Å / Relative weight: 1
ReflectionResolution: 2.14→47.4 Å / Num. obs: 43575 / % possible obs: 99.1 % / Redundancy: 24.2 % / Biso Wilson estimate: 47.74 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.08 / Net I/σ(I): 21.9
Reflection shellResolution: 2.14→2.25 Å / Rmerge(I) obs: 1.38 / Num. unique obs: 23727 / CC1/2: 0.81

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.14→47.4 Å / SU ML: 0.2982 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.0603
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2316 2212 5.08 %
Rwork0.1946 41363 -
obs0.1965 43575 98.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 70.33 Å2
Refinement stepCycle: LAST / Resolution: 2.14→47.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2587 0 16 109 2712
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00352670
X-RAY DIFFRACTIONf_angle_d0.64713635
X-RAY DIFFRACTIONf_chiral_restr0.0435403
X-RAY DIFFRACTIONf_plane_restr0.0058489
X-RAY DIFFRACTIONf_dihedral_angle_d6.0093383
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.14-2.180.38051030.36732324X-RAY DIFFRACTION88.74
2.18-2.230.32531480.3482552X-RAY DIFFRACTION96.84
2.23-2.290.33221500.29172534X-RAY DIFFRACTION98.24
2.29-2.350.36731280.25192610X-RAY DIFFRACTION99.38
2.35-2.420.25051320.22682625X-RAY DIFFRACTION99.46
2.42-2.50.25421460.22252608X-RAY DIFFRACTION99.42
2.5-2.590.26281470.22722574X-RAY DIFFRACTION99.6
2.59-2.690.27441520.22322612X-RAY DIFFRACTION99.75
2.69-2.810.33361030.22962640X-RAY DIFFRACTION99.82
2.81-2.960.26791170.21142614X-RAY DIFFRACTION99.82
2.96-3.150.20321400.21332641X-RAY DIFFRACTION99.86
3.15-3.390.22211470.23562589X-RAY DIFFRACTION100
3.39-3.730.26891710.18472603X-RAY DIFFRACTION99.96
3.73-4.270.21411500.16142594X-RAY DIFFRACTION100
4.27-5.380.20261320.15192630X-RAY DIFFRACTION100
5.38-47.40.16791460.16522613X-RAY DIFFRACTION99.89
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)
11.395544805340.2344632533370.6154531720471.59586850008-0.3301356057353.052907679860.0145914005141-0.1076176828370.05361975969260.171132409417-0.0398254893861-0.136714216314-0.06462072522940.1368695944880.02428434076920.273465829237-0.0141358429984-0.01045862137580.282265514284-0.02004481860420.304987833121-7.97086219731-14.7014891996.95571298495
22.28993989631-0.502095554456-0.3387912984323.96689252509-0.2392954287691.85151502317-0.0459974997754-0.012914076887-0.2185595367130.1509854369540.0284267666836-1.042096754550.1658813295880.806186675830.02058952931870.4106591785590.0842109442645-0.01017822626310.657400766042-0.06914589085570.6121432809086.09628494143-30.1276211658-10.7450177102
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 3 through 148 )3 - 1482 - 147
22chain 'A' and (resid 149 through 339 )149 - 339148 - 338

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