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- PDB-3i9f: Crystal structure of a putative type 11 methyltransferase from Su... -

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Basic information

Entry
Database: PDB / ID: 3i9f
TitleCrystal structure of a putative type 11 methyltransferase from Sulfolobus solfataricus
ComponentsPutative type 11 methyltransferase
KeywordsTRANSFERASE / STRUCTURAL GENOMICS / PSI-2 / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC
Function / homology
Function and homology information


S-adenosylmethionine-dependent methyltransferase activity / methyltransferase activity / metal ion binding
Similarity search - Function
Methyltransferase type 11 / 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
Methyltransferase type 11 domain-containing protein
Similarity search - Component
Biological speciesSulfolobus solfataricus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.5 Å
AuthorsBonanno, J.B. / Dickey, M. / Bain, K.T. / Chang, S. / Ozyurt, S. / Sauder, J.M. / Burley, S.K. / Almo, S.C. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: To be Published
Title: Crystal structure of a putative type 11 methyltransferase from Sulfolobus solfataricus
Authors: Bonanno, J.B. / Dickey, M. / Bain, K.T. / Chang, S. / Ozyurt, S. / Sauder, J.M. / Burley, S.K. / Almo, S.C.
History
DepositionJul 10, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 28, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 1.3Nov 21, 2018Group: Data collection / Structure summary / Category: audit_author / Item: _audit_author.identifier_ORCID
Revision 1.4Feb 10, 2021Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author ...audit_author / citation_author / struct_ref_seq_dif / struct_site
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Feb 21, 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

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Assembly

Deposited unit
A: Putative type 11 methyltransferase
B: Putative type 11 methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,1508
Polymers39,7582
Non-polymers3926
Water55831
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Putative type 11 methyltransferase
hetero molecules

A: Putative type 11 methyltransferase
hetero molecules

A: Putative type 11 methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,22512
Polymers59,6363
Non-polymers5899
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
Buried area4160 Å2
ΔGint-171 kcal/mol
Surface area23110 Å2
MethodPISA
3
B: Putative type 11 methyltransferase
hetero molecules

B: Putative type 11 methyltransferase
hetero molecules

B: Putative type 11 methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,22512
Polymers59,6363
Non-polymers5899
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
Buried area4110 Å2
ΔGint-173 kcal/mol
Surface area23110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)116.728, 116.728, 116.728
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number198
Space group name H-MP213
Components on special symmetry positions
IDModelComponents
11A-2-

ZN

21B-4-

ZN

31A-196-

HOH

41B-194-

HOH

DetailsProbable biological dimer, crystallographic hexamer mediated by His6 tag and Zn

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Components

#1: Protein Putative type 11 methyltransferase


Mass: 19878.766 Da / Num. of mol.: 2 / Fragment: sequence database residues 18-176
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus solfataricus (archaea) / Gene: SSO1178 / Plasmid: modified pET26 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q97YX4
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 31 / 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: 3.33 Å3/Da / Density % sol: 63.1 %
Crystal growTemperature: 294 K / Method: vapor diffusion / pH: 7
Details: 20% PEG 3350, 200mM potassium nitrate, pH 7.0, vapor diffusion, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.97958 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 7, 2009
RadiationMonochromator: diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97958 Å / Relative weight: 1
ReflectionResolution: 2.5→36.913 Å / Num. all: 18652 / Num. obs: 18652 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 18.9 % / Biso Wilson estimate: 53.8 Å2 / Rmerge(I) obs: 0.154 / Rsym value: 0.154 / Net I/σ(I): 15.1
Reflection shellResolution: 2.5→2.64 Å / Redundancy: 19 % / Rmerge(I) obs: 0.803 / Mean I/σ(I) obs: 4.4 / Num. unique all: 2682 / Rsym value: 0.803 / % possible all: 100

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Processing

Software
NameVersionClassificationNB
SCALA3.3.9data scaling
REFMACrefinement
PDB_EXTRACT3.005data extraction
MAR345CCDdata collection
MOSFLMdata reduction
SHELXCDphasing
SHELXEmodel building
RefinementMethod to determine structure: SAD / Resolution: 2.5→20 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.91 / WRfactor Rfree: 0.255 / WRfactor Rwork: 0.21 / Occupancy max: 1 / Occupancy min: 0.33 / FOM work R set: 0.842 / SU B: 7.683 / SU ML: 0.176 / SU R Cruickshank DPI: 0.351 / SU Rfree: 0.258 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.351 / ESU R Free: 0.258 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS; METALS MODELED AS ZN BASED ON ANOMALOUS DIFFERENCE FOURIER PEAKS AND GEOMETRY
RfactorNum. reflection% reflectionSelection details
Rfree0.257 905 4.9 %RANDOM
Rwork0.215 ---
obs0.217 18586 100 %-
all-18586 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 80.92 Å2 / Biso mean: 48.937 Å2 / Biso min: 21 Å2
Refinement stepCycle: LAST / Resolution: 2.5→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2718 0 6 31 2755
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0222796
X-RAY DIFFRACTIONr_bond_other_d0.0010.021916
X-RAY DIFFRACTIONr_angle_refined_deg1.5341.9413783
X-RAY DIFFRACTIONr_angle_other_deg0.89634664
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3355336
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.54224.101139
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.9815477
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.9061512
X-RAY DIFFRACTIONr_chiral_restr0.0910.2399
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0213103
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02589
X-RAY DIFFRACTIONr_mcbond_it0.9461.51668
X-RAY DIFFRACTIONr_mcbond_other0.1411.5677
X-RAY DIFFRACTIONr_mcangle_it1.83422702
X-RAY DIFFRACTIONr_scbond_it2.33231128
X-RAY DIFFRACTIONr_scangle_it3.6264.51079
LS refinement shellResolution: 2.5→2.564 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.239 75 -
Rwork0.259 1265 -
all-1340 -
obs-1265 100 %

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