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- PDB-1fbn: CRYSTAL STRUCTURE OF A FIBRILLARIN HOMOLOGUE FROM METHANOCOCCUS J... -

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Basic information

Entry
Database: PDB / ID: 1fbn
TitleCRYSTAL STRUCTURE OF A FIBRILLARIN HOMOLOGUE FROM METHANOCOCCUS JANNASCHII, A HYPERTHERMOPHILE, AT 1.6 A
ComponentsMJ FIBRILLARIN HOMOLOGUE
KeywordsRIBOSOME / FIBRILLARIN / MJ PROTEINS / RIBOSOMAL RNA PROCESSING / SNORNP / Structural Genomics / BSGC structure funded by NIH / Protein Structure Initiative / PSI / Berkeley Structural Genomics Center
Function / homology
Function and homology information


histone H2AQ104 methyltransferase activity / box C/D sno(s)RNA 3'-end processing / rRNA methyltransferase activity / box C/D methylation guide snoRNP complex / rRNA methylation / tRNA processing / Transferases; Transferring one-carbon groups; Methyltransferases / 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
Fibrillarin-like rRNA/tRNA 2'-O-methyltransferase
Similarity search - Component
Biological speciesMethanocaldococcus jannaschii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIRAS / Resolution: 1.6 Å
AuthorsWang, H. / Boisvert, D. / Kim, K.K. / Kim, R. / Kim, S.H. / Berkeley Structural Genomics Center (BSGC)
CitationJournal: EMBO J. / Year: 2000
Title: Crystal structure of a fibrillarin homologue from Methanococcus jannaschii, a hyperthermophile, at 1.6 A resolution.
Authors: Wang, H. / Boisvert, D. / Kim, K.K. / Kim, R. / Kim, S.H.
History
DepositionApr 25, 1999Deposition site: BNL / Processing site: RCSB
Revision 1.0Apr 26, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 26, 2014Group: Other

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: MJ FIBRILLARIN HOMOLOGUE


Theoretical massNumber of molelcules
Total (without water)26,2401
Polymers26,2401
Non-polymers00
Water3,351186
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)121.407, 43.264, 55.303
Angle α, β, γ (deg.)90.00, 96.99, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein MJ FIBRILLARIN HOMOLOGUE


Mass: 26239.734 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanocaldococcus jannaschii (archaea)
Plasmid: PET21A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / Variant (production host): PSJ1240 / References: UniProt: Q58108
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 186 / 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: 2.78 Å3/Da / Density % sol: 55.22 %
Crystal growpH: 5.6
Details: 20% 2-PROPANOL, 20% PEG4k, 0.1M SODIUM CITRATE, pH 5.6
Crystal grow
*PLUS
Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
125 mg/mlprotein1drop
210 %PEG40001drop
310 %isopropanol1drop
40.05 Msodium citrate1drop
520 %PEG40001reservoir
620 %isopropanol1reservoir
70.1 Msodium citrate1reservoir

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Data collection

DiffractionMean temperature: 170 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.97921,0.97894,0.96373
DetectorDate: Oct 1, 1997
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979211
20.978941
30.963731
ReflectionResolution: 1.6→30 Å / Num. obs: 37155 / % possible obs: 97 % / Redundancy: 2 % / Biso Wilson estimate: 28.3 Å2 / Rsym value: 0.076
Reflection shellResolution: 1.6→1.66 Å / Redundancy: 2.5 % / Rsym value: 0.4 / % possible all: 95.8
Reflection
*PLUS
Rmerge(I) obs: 0.076

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: MIRAS / Resolution: 1.6→12 Å / Rfactor Rfree error: 0.004 / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.248 3645 10.2 %RANDOM
Rwork0.229 ---
obs-35943 95.2 %-
Displacement parametersBiso mean: 32.9 Å2
Baniso -1Baniso -2Baniso -3
1-5.34 Å20 Å22.94 Å2
2---6.52 Å20 Å2
3---0.99 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.28 Å0.25 Å
Luzzati d res low-5 Å
Luzzati sigma a0.13 Å0.27 Å
Refinement stepCycle: LAST / Resolution: 1.6→12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1829 0 0 186 2015
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d24.6
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.71
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it2.551.5
X-RAY DIFFRACTIONc_mcangle_it2.732
X-RAY DIFFRACTIONc_scbond_it5.822
X-RAY DIFFRACTIONc_scangle_it5.342.5
LS refinement shellResolution: 1.6→1.7 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.381 548 10 %
Rwork0.381 4908 -
obs--87.8 %
Software
*PLUS
Name: CNS / Version: 3 / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.6 Å / Lowest resolution: 12 Å / σ(F): 0 / % reflection Rfree: 10.2 % / Rfactor obs: 0.229
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 32.9 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg24.6
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.71
X-RAY DIFFRACTIONc_mcbond_it2.551.5
X-RAY DIFFRACTIONc_scbond_it5.822
X-RAY DIFFRACTIONc_mcangle_it2.732
X-RAY DIFFRACTIONc_scangle_it5.342.5
LS refinement shell
*PLUS
Highest resolution: 1.6 Å / Lowest resolution: 1.7 Å / Rfactor Rfree: 0.381 / % reflection Rfree: 10 % / Rfactor Rwork: 0.381

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