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- PDB-8bvi: Crystal structure of the METTL9-like histidine methyltransferase ... -

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Basic information

Entry
Database: PDB / ID: 8bvi
TitleCrystal structure of the METTL9-like histidine methyltransferase from Ostreococcus tauri
ComponentsDREV methyltransferase
KeywordsTRANSFERASE / methyltransferase / histidine methyltransferase / Rossmann fold
Function / homologyprotein-L-histidine N-pros-methyltransferase activity / Protein-L-histidine N-pros-methyltransferase / DREV methyltransferase / methylation / S-adenosyl-L-methionine-dependent methyltransferase superfamily / DREV methyltransferase
Function and homology information
Biological speciesOstreococcus tauri (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsHammerstad, M. / Schroer, L. / Hersleth, H.-P.
Funding support Norway, 1items
OrganizationGrant numberCountry
Research Council of Norway Norway
CitationJournal: To be published
Title: METTL9-like histidine methyltransferases
Authors: Schroer, L. / Hammerstad, M. / Weirich, S. / Hersleth, H.-P. / Groensberg, I.A. / Hagen, L. / Slupphaug, G. / Davydova, E. / Falnes, P.O.
History
DepositionDec 4, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 13, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DREV methyltransferase


Theoretical massNumber of molelcules
Total (without water)33,9021
Polymers33,9021
Non-polymers00
Water1086
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area16040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.898, 106.898, 106.898
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number198
Space group name H-MP213
Space group name HallP2ac2ab3
Symmetry operation#1: x,y,z
#2: z,x,y
#3: y,z,x
#4: -y+1/2,-z,x+1/2
#5: z+1/2,-x+1/2,-y
#6: -y,z+1/2,-x+1/2
#7: -z+1/2,-x,y+1/2
#8: -z,x+1/2,-y+1/2
#9: y+1/2,-z+1/2,-x
#10: x+1/2,-y+1/2,-z
#11: -x,y+1/2,-z+1/2
#12: -x+1/2,-y,z+1/2
Components on special symmetry positions
IDModelComponents
11A-401-

HOH

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Components

#1: Protein DREV methyltransferase / Methyltransferase-like protein 9


Mass: 33902.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Methyltransferase-like protein 9 / Source: (gene. exp.) Ostreococcus tauri (plant) / Gene: OT_ostta03g04640 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q01C52
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Formula: H2O

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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: 2.97 Å3/Da / Density % sol: 58.6 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1 M Hepes pH 7.5, 0.2 M L-proline, 10% w/v polyethylene glycol 3,350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.918402 Å
DetectorType: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Oct 5, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918402 Å / Relative weight: 1
ReflectionResolution: 3.1→75.59 Å / Num. obs: 7642 / % possible obs: 100 % / Redundancy: 9.4 % / Biso Wilson estimate: 119.69 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.117 / Rpim(I) all: 0.041 / Rrim(I) all: 0.124 / Χ2: 1 / Net I/σ(I): 10.5
Reflection shellResolution: 3.1→3.31 Å / Redundancy: 9.4 % / Rmerge(I) obs: 1.9 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 1372 / CC1/2: 0.553 / Rpim(I) all: 0.648 / Rrim(I) all: 2.01 / Χ2: 1 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
REFMAC5.8.0352refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.1→47.81 Å / SU ML: 0.4073 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 35.4375
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2801 435 5.72 %
Rwork0.2225 7172 -
obs0.2258 7607 99.87 %
Solvent computationShrinkage radii: 0.6 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 131.37 Å2
Refinement stepCycle: LAST / Resolution: 3.1→47.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2299 0 0 6 2305
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00112335
X-RAY DIFFRACTIONf_angle_d0.33183159
X-RAY DIFFRACTIONf_chiral_restr0.0378358
X-RAY DIFFRACTIONf_plane_restr0.0027420
X-RAY DIFFRACTIONf_dihedral_angle_d7.8864869
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1-3.310.37591350.32832352X-RAY DIFFRACTION99.84
3.31-4.470.28871360.26242377X-RAY DIFFRACTION100
4.47-47.810.2631640.19022443X-RAY DIFFRACTION99.77
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)
11.77200022522-0.07760560962570.8521347970393.603032620031.447425663513.320894124120.3497103710170.176507004406-0.220179917631-0.226462187731-0.1179180791650.2923173530010.257860375186-0.17980267716-0.1772673999070.8565152166160.0398668525555-0.007678016204460.9730351253840.05920312212570.83295914983-1.9410802081329.58415692662.83278874435
26.61559867107-2.639308802580.6914228277885.95802540727-0.6783967856862.763898151740.3639969384670.567020175354-0.222250152781-0.5088364008620.0507229194989-0.3881653232170.07480187605130.349214749941-0.3894797847211.077249375960.114721556596-0.1479702294481.0148056592-0.2599690009770.7177618582517.0535603454114.2129488823-11.8855911941
34.2541663178-0.5035612890360.2125302117153.681920891651.58851647897.623135651320.5115969745540.8943659724540.557833158793-1.32324139776-0.0937138239767-0.692005327461-0.6231225999320.265425239217-0.3978869971791.475929235110.240505986921-0.007161346734450.9592964329540.09900268493920.9055475988473.6655654595331.9099099722-11.4560745025
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 7 through 111 )7 - 1111 - 105
22chain 'A' and (resid 112 through 225 )112 - 225106 - 219
33chain 'A' and (resid 226 through 305 )226 - 305220 - 299

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