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- PDB-4df3: Crystal Structure of Aeropyrum pernix fibrillarin in complex with... -

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Basic information

Entry
Database: PDB / ID: 4df3
TitleCrystal Structure of Aeropyrum pernix fibrillarin in complex with natively bound S-adenosyl-L-methionine at 1.7A
ComponentsFibrillarin-like rRNA/tRNA 2'-O-methyltransferase
KeywordsTRANSFERASE / NADP Rossmann Superfamily / methyltransferase / S-adenosyl-L-methionine (SAM) binding / nucleolus
Function / homology
Function and homology information


tRNA processing / Transferases; Transferring one-carbon groups; Methyltransferases / methyltransferase activity / rRNA processing / methylation / RNA binding
Similarity search - Function
rRNA 2'-O-methyltransferase fibrillarin-like / Fibrillarin, conserved site / Fibrillarin / Fibrillarin signature. / Fibrillarin / Vaccinia Virus protein VP39 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold ...rRNA 2'-O-methyltransferase fibrillarin-like / Fibrillarin, conserved site / Fibrillarin / Fibrillarin signature. / Fibrillarin / Vaccinia Virus protein VP39 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
S-ADENOSYLMETHIONINE / Fibrillarin-like rRNA/tRNA 2'-O-methyltransferase
Similarity search - Component
Biological speciesAeropyrum pernix (archaea)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.73 Å
Authorsde Silva, U.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2012
Title: Structure of Aeropyrum pernix fibrillarin in complex with natively bound S-adenosyl-L-methionine at 1.7 A resolution.
Authors: de Silva, U. / Zhou, Z. / Brown, B.A.
History
DepositionJan 22, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 8, 2012Provider: repository / Type: Initial release
Revision 1.1Feb 20, 2013Group: Database references
Revision 1.2Jul 17, 2019Group: Data collection / Refinement description / Category: software
Item: _software.classification / _software.name / _software.version
Revision 1.3Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Fibrillarin-like rRNA/tRNA 2'-O-methyltransferase
B: Fibrillarin-like rRNA/tRNA 2'-O-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,1954
Polymers53,3982
Non-polymers7972
Water6,017334
1
A: Fibrillarin-like rRNA/tRNA 2'-O-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,0972
Polymers26,6991
Non-polymers3981
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Fibrillarin-like rRNA/tRNA 2'-O-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,0972
Polymers26,6991
Non-polymers3981
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)39.639, 52.087, 63.030
Angle α, β, γ (deg.)66.28, 84.55, 77.61
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Fibrillarin-like rRNA/tRNA 2'-O-methyltransferase


Mass: 26698.832 Da / Num. of mol.: 2 / Mutation: R8S, E9R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aeropyrum pernix (archaea) / Gene: flpA, APE_2196 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9Y9U3, Transferases; Transferring one-carbon groups; Methyltransferases
#2: Chemical ChemComp-SAM / S-ADENOSYLMETHIONINE / S-Adenosyl methionine


Mass: 398.437 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H22N6O5S
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 334 / 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: 2.22 Å3/Da / Density % sol: 44.5 %
Crystal growTemperature: 296.15 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 20mM Tris.HCL pH8, 150mM NaCl, 200mM Imidazole, 20mM Tris.HCl pH7, 5% Isopropanol, 10% PEG 4000, pH 6.5, Vapor DIffusion, Sitting Drop, temperature 296.15K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.54187 Å
DetectorType: RIGAKU SATURN 92 / Detector: CCD / Date: May 1, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54187 Å / Relative weight: 1
ReflectionResolution: 1.73→46.78 Å / Num. obs: 47059 / % possible obs: 90.6 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1 / Redundancy: 9.1 % / Rmerge(I) obs: 0.066 / Net I/σ(I): 0.189

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Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
CNSrefinement
CrystalCleardata collection
d*TREKdata reduction
d*TREKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.73→46.78 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.931 / SU B: 2.608 / SU ML: 0.086 / Cross valid method: THROUGHOUT / ESU R: 0.14 / ESU R Free: 0.136 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2335 2163 5.1 %RANDOM
Rwork0.1871 ---
obs0.18954 40488 90.64 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.715 Å2
Baniso -1Baniso -2Baniso -3
1-0.05 Å20 Å2-0.06 Å2
2---0.09 Å20.08 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.73→46.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3694 0 54 334 4082
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0223824
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.9071.9855170
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3335458
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.39221.739184
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.02715662
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.4151550
X-RAY DIFFRACTIONr_chiral_restr0.1430.2566
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0212902
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.3761.52288
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.31823686
X-RAY DIFFRACTIONr_scbond_it3.5931536
X-RAY DIFFRACTIONr_scangle_it5.6494.51484
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.73→1.775 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.417 94 -
Rwork0.357 1635 -
obs--49.9 %

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