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- PDB-5fa8: SAM complex with aKMT from the hyperthermophilic archaeon Sulfolo... -

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Basic information

Entry
Database: PDB / ID: 5fa8
TitleSAM complex with aKMT from the hyperthermophilic archaeon Sulfolobus islandicu
ComponentsRibosomal protein L11 methyltransferase, putativeRibosome
KeywordsTRANSFERASE / protein methyltransferase
Function / homology
Function and homology information


protein-lysine N-methyltransferase activity / methylation / ribosome / metal ion binding
Similarity search - Function
N-lysine methyltransferase FAM173A/B / Methyltransferase domain / Methyltransferase domain / Vaccinia Virus protein VP39 / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
S-ADENOSYLMETHIONINE / Ribosomal protein L11 methyltransferase, putative
Similarity search - Component
Biological speciesSulfolobus islandicus (acidophilic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.3 Å
AuthorsOuyang, S.
Funding support China, 1items
OrganizationGrant numberCountry
the National Natural Science Foundation of China31570875, 31330019, 81590761 and 31200559 China
CitationJournal: Mol.Cell Proteomics / Year: 2016
Title: aKMT Catalyzes Extensive Protein Lysine Methylation in the Hyperthermophilic Archaeon Sulfolobus islandicus but is Dispensable for the Growth of the Organism
Authors: Chu, Y. / Zhu, Y. / Chen, Y. / Li, W. / Zhang, Z. / Liu, D. / Wang, T. / Ma, J. / Deng, H. / Liu, Z.J. / Ouyang, S. / Huang, L.
History
DepositionDec 11, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 29, 2016Provider: repository / Type: Initial release
Revision 1.1Jul 6, 2016Group: Database references
Revision 1.2Jul 27, 2016Group: Database references
Revision 1.3Sep 14, 2016Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ribosomal protein L11 methyltransferase, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,8373
Polymers18,4141
Non-polymers4232
Water3,873215
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area80 Å2
ΔGint-7 kcal/mol
Surface area8130 Å2
2
A: Ribosomal protein L11 methyltransferase, putative
hetero molecules

A: Ribosomal protein L11 methyltransferase, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,6746
Polymers36,8292
Non-polymers8454
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area2440 Å2
ΔGint-31 kcal/mol
Surface area13980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.301, 57.993, 55.725
Angle α, β, γ (deg.)90.00, 100.93, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-500-

HOH

21A-611-

HOH

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Components

#1: Protein Ribosomal protein L11 methyltransferase, putative / Ribosome


Mass: 18414.469 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus islandicus (strain M.14.25 / Kamchatka #1) (acidophilic)
Strain: M.14.25 / Kamchatka #1 / Gene: M1425_1574 / Production host: Escherichia coli (E. coli) / References: UniProt: C3MWA1
#2: Chemical ChemComp-SAM / S-ADENOSYLMETHIONINE / S-Adenosyl methionine


Mass: 398.437 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H22N6O5S
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 215 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.11 Å3/Da / Density % sol: 41.64 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop
Details: 10mM magnesium chloride hexahydrate, 0.1M HEPES-NaOH, pH 7.0, 15%(w/v) polyethylene glycol 3,350, 5mM nickel chloride hexahydrate

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 18, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.3→28.6 Å / Num. obs: 69363 / % possible obs: 95.5 % / Redundancy: 7 % / Net I/σ(I): 2.1

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data processing
RefinementMethod to determine structure: SAD / Resolution: 1.3→28.6 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 22.35 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2124 3909 5.64 %
Rwork0.1831 --
obs0.1848 69363 94.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.3→28.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1233 0 28 215 1476
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061283
X-RAY DIFFRACTIONf_angle_d1.2221739
X-RAY DIFFRACTIONf_dihedral_angle_d13.499490
X-RAY DIFFRACTIONf_chiral_restr0.049202
X-RAY DIFFRACTIONf_plane_restr0.005220
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.299-1.31480.3889780.29321338X-RAY DIFFRACTION55
1.3148-1.33150.27671020.2811666X-RAY DIFFRACTION68
1.3315-1.3490.25071320.27242147X-RAY DIFFRACTION83
1.349-1.36750.29671350.24582254X-RAY DIFFRACTION94
1.3675-1.3870.26741420.21962358X-RAY DIFFRACTION95
1.387-1.40770.2641430.22212391X-RAY DIFFRACTION97
1.4077-1.42970.24181450.22082392X-RAY DIFFRACTION97
1.4297-1.45310.25571410.21122417X-RAY DIFFRACTION97
1.4531-1.47820.26411440.19812393X-RAY DIFFRACTION97
1.4782-1.50510.22461440.19452426X-RAY DIFFRACTION97
1.5051-1.5340.25721360.19332345X-RAY DIFFRACTION98
1.534-1.56530.19711470.18032438X-RAY DIFFRACTION97
1.5653-1.59930.20521420.17422399X-RAY DIFFRACTION98
1.5993-1.63660.19291460.17632449X-RAY DIFFRACTION98
1.6366-1.67750.23271410.1742384X-RAY DIFFRACTION98
1.6775-1.72280.23731470.18372461X-RAY DIFFRACTION98
1.7228-1.77350.16731470.18242427X-RAY DIFFRACTION99
1.7735-1.83070.20291440.18562426X-RAY DIFFRACTION99
1.8307-1.89620.24271450.17262409X-RAY DIFFRACTION99
1.8962-1.97210.19341470.16232502X-RAY DIFFRACTION99
1.9721-2.06180.20361450.16152450X-RAY DIFFRACTION99
2.0618-2.17050.18071450.16912445X-RAY DIFFRACTION99
2.1705-2.30640.21841450.17052463X-RAY DIFFRACTION99
2.3064-2.48440.22611480.18122435X-RAY DIFFRACTION99
2.4844-2.73420.19631460.19412480X-RAY DIFFRACTION99
2.7342-3.12940.21081490.18672433X-RAY DIFFRACTION99
3.1294-3.94110.19161450.16642401X-RAY DIFFRACTION98
3.9411-28.6110.21621380.18922325X-RAY DIFFRACTION94

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