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- PDB-6f5z: Complex between the Haloferax volcanii Trm112 methyltransferase a... -

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Basic information

Entry
Database: PDB / ID: 6f5z
TitleComplex between the Haloferax volcanii Trm112 methyltransferase activator and the Hvo_0019 putative methyltransferase
Components
  • 24-sterol C-methyltransferase
  • UPF0434 family protein
KeywordsTRANSFERASE / Protein complex / Holoenzyme / methyltransferase / halophile / archaea
Function / homology
Function and homology information


sterol 24-C-methyltransferase activity / sterol biosynthetic process / Transferases; Transferring one-carbon groups; Methyltransferases / methyltransferase activity / methylation
Similarity search - Function
: / Trm112-like / Trm112p-like protein / Methyltransferase type 11 / Methyltransferase domain / S-adenosyl-L-methionine-dependent methyltransferase superfamily
Similarity search - Domain/homology
S-ADENOSYL-L-HOMOCYSTEINE / Methyltransferase activator Trm112 / S-adenosylmethionine-dependent methyltransferase / S-adenosylmethionine-dependent methyltransferase
Similarity search - Component
Biological speciesHaloferax volcanii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.35 Å
AuthorsGraille, M. / van Tran, N.
Funding support France, 1items
OrganizationGrant numberCountry
French National Research AgencyANR-14-CE09-0016-02 France
CitationJournal: Nucleic Acids Res. / Year: 2018
Title: Evolutionary insights into Trm112-methyltransferase holoenzymes involved in translation between archaea and eukaryotes.
Authors: van Tran, N. / Muller, L. / Ross, R.L. / Lestini, R. / Letoquart, J. / Ulryck, N. / Limbach, P.A. / de Crecy-Lagard, V. / Cianferani, S. / Graille, M.
History
DepositionDec 4, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 11, 2018Provider: repository / Type: Initial release
Revision 1.1Jul 25, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Oct 3, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 24-sterol C-methyltransferase
B: 24-sterol C-methyltransferase
C: UPF0434 family protein
D: UPF0434 family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,2848
Polymers66,3314
Non-polymers9534
Water6,972387
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering, SEC-MALLS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6070 Å2
ΔGint-29 kcal/mol
Surface area22830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.610, 82.290, 88.030
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein 24-sterol C-methyltransferase


Mass: 26301.711 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Haloferax volcanii (archaea)
Strain: ATCC 29605 / DSM 3757 / JCM 8879 / NBRC 14742 / NCIMB 2012 / VKM B-1768 / DS2
Gene: C498_18333
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: L9UJ72, UniProt: D4GYL4*PLUS
#2: Protein UPF0434 family protein


Mass: 6863.661 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Haloferax volcanii (strain ATCC 29605 / DSM 3757 / JCM 8879 / NBRC 14742 / NCIMB 2012 / VKM B-1768 / DS2) (archaea)
Strain: ATCC 29605 / DSM 3757 / JCM 8879 / NBRC 14742 / NCIMB 2012 / VKM B-1768 / DS2
Gene: HVO_1131
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: D4GW82
#3: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H20N6O5S
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 387 / 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: 2.2 Å3/Da / Density % sol: 44.11 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: 0.1-0.3 M NaCl; 0.1 M Bis-Tris pH 5,5, 20-25% w/v PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.98007 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 9, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98007 Å / Relative weight: 1
ReflectionResolution: 1.35→48.19 Å / Num. obs: 128740 / % possible obs: 100 % / Redundancy: 12.326 % / Biso Wilson estimate: 19.11 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.084 / Rrim(I) all: 0.087 / Χ2: 1.015 / Net I/σ(I): 14.41 / Num. measured all: 1586836 / Scaling rejects: 639
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.35-1.3912.1171.7281.3194340.3061.804100
1.39-1.4212.0681.6381.4291920.3891.711100
1.42-1.4611.9891.371.7689380.5111.432100
1.46-1.5111.861.1622.0786850.6631.215100
1.51-1.5611.5330.9412.6184480.7750.985100
1.56-1.6110.8580.7873.1981530.8380.827100
1.61-1.6711.6210.6034.4778570.9080.631100
1.67-1.7411.5220.4486.0576000.9530.469100
1.74-1.8212.5570.3258.6372790.9780.339100
1.82-1.9112.5510.23611.669950.9880.246100
1.91-2.0112.4590.16615.9366700.9940.174100
2.01-2.1312.3750.12420.3262870.9960.129100
2.13-2.2812.2160.09425.3459090.9970.098100
2.28-2.4611.9410.07728.8755330.9980.081100
2.46-2.711.0980.06531.9651240.9990.069100
2.7-3.0211.0020.05436.1146450.9990.057100
3.02-3.4911.4910.04343.8641070.9990.045100
3.49-4.2715.7780.04455.6235270.9990.046100
4.27-6.0425.0130.05167.03276010.052100
6.04-48.1917.7860.04554.65159710.04699.8

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
SOLVEphasing
RESOLVEphasing
BUSTER2.10.3refinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: SAD / Resolution: 1.35→48.19 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.953 / SU R Cruickshank DPI: 0.054 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.055 / SU Rfree Blow DPI: 0.056 / SU Rfree Cruickshank DPI: 0.055
RfactorNum. reflection% reflectionSelection details
Rfree0.207 6437 5 %RANDOM
Rwork0.185 ---
obs0.186 128738 100 %-
Displacement parametersBiso max: 96.34 Å2 / Biso mean: 23.86 Å2 / Biso min: 11.1 Å2
Baniso -1Baniso -2Baniso -3
1--2.2357 Å20 Å20 Å2
2--2.3425 Å20 Å2
3----0.1068 Å2
Refine analyzeLuzzati coordinate error obs: 0.19 Å
Refinement stepCycle: final / Resolution: 1.35→48.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4529 0 64 387 4980
Biso mean--25.17 32.62 -
Num. residues----568
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1648SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes141HARMONIC2
X-RAY DIFFRACTIONt_gen_planes733HARMONIC5
X-RAY DIFFRACTIONt_it4780HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion608SEMIHARMONIC5
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_contact5939SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d4780HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg6512HARMONIC20.98
X-RAY DIFFRACTIONt_omega_torsion3.91
X-RAY DIFFRACTIONt_other_torsion16.36
LS refinement shellResolution: 1.35→1.39 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2409 471 5 %
Rwork0.2305 8951 -
all0.2311 9422 -
obs--99.96 %

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