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- PDB-3evz: Crystal structure of Methyltransferase from Pyrococcus furiosus -

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Basic information

Entry
Database: PDB / ID: 3evz
TitleCrystal structure of Methyltransferase from Pyrococcus furiosus
Componentsmethyltransferase
KeywordsTRANSFERASE / 11120i / Methyltransferase / NYSGXRC / New York SGX Research Center for Structural Genomics / Protein Structure Initiative / Pyrococcus furiosus / PSI-2
Function / homology
Function and homology information


23S rRNA (adenine(1618)-N(6))-methyltransferase activity / rRNA base methylation
Similarity search - Function
METTL16/RlmF family / Methyltransferase domain 25 / 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 domain-containing protein
Similarity search - Component
Biological speciesPyrococcus furiosus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.2 Å
AuthorsZhang, Z. / Eswaramoorthy, S. / Burley, S.K. / Swaminathan, S. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: To be Published
Title: Crystal structure of methyltransferase from Pyrococcus furiosus
Authors: Zhang, Z. / Eswaramoorthy, S. / Burley, S.K. / Swaminathan, S.
History
DepositionOct 13, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 11, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2Dec 21, 2016Group: Structure summary
Revision 1.3Feb 10, 2021Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author / struct_conn
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Dec 27, 2023Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.5Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: methyltransferase


Theoretical massNumber of molelcules
Total (without water)26,2471
Polymers26,2471
Non-polymers00
Water91951
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)46.877, 46.877, 331.412
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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Components

#1: Protein methyltransferase


Mass: 26246.688 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus furiosus (archaea) / Gene: PF0847 / Plasmid: BC-pSGX3(BC) / Production host: Escherichia coli (E. coli) / Strain (production host): DE3 / References: UniProt: Q8U2I7
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 51 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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 Å3/Da / Density % sol: 38.57 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: D9. 0.1 M Tris pH 8.5, 25% w/v PEG 3350, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.9792
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Oct 1, 2008 / Details: mirrors
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.2→55.22 Å / Num. all: 11261 / Num. obs: 10605 / % possible obs: 92.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 28.4 % / Rmerge(I) obs: 0.111 / Rsym value: 0.114 / Net I/σ(I): 29.1
Reflection shellResolution: 2.2→2.26 Å / Redundancy: 27.2 % / Rmerge(I) obs: 0.331 / Mean I/σ(I) obs: 8.6 / Rsym value: 0.342 / % possible all: 85

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Processing

Software
NameVersionClassification
CBASSdata collection
SHELXSphasing
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.2→55.22 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.913 / SU B: 12.973 / SU ML: 0.162 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.289 / ESU R Free: 0.233 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.259 535 4.8 %RANDOM
Rwork0.19916 ---
obs0.20195 10605 92.38 %-
all-11261 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 33.206 Å2
Baniso -1Baniso -2Baniso -3
1-1.02 Å20.51 Å20 Å2
2--1.02 Å20 Å2
3----1.53 Å2
Refinement stepCycle: LAST / Resolution: 2.2→55.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1575 0 0 51 1626
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.0221611
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.1021.9652162
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2635194
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.74423.01473
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.40715292
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.7971511
X-RAY DIFFRACTIONr_chiral_restr0.1810.2234
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021198
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2510.2722
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.320.21073
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1820.282
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2180.242
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.190.212
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.3061.5999
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.91121553
X-RAY DIFFRACTIONr_scbond_it3.3733695
X-RAY DIFFRACTIONr_scangle_it5.1544.5609
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.287 40 -
Rwork0.192 638 -
obs--78.56 %
Refinement TLS params.Method: refined / Origin x: 15.699 Å / Origin y: 8.171 Å / Origin z: -14.643 Å
111213212223313233
T-0.015 Å2-0.0414 Å2-0.0103 Å2--0.1178 Å20.0123 Å2---0.2094 Å2
L0.7455 °21.2563 °2-0.474 °2-3.9613 °20.0224 °2--3.109 °2
S0.0148 Å °-0.0571 Å °0.0284 Å °0.1301 Å °0.0224 Å °-0.2421 Å °-0.122 Å °0.1912 Å °-0.0373 Å °

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