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- PDB-1pry: Structure Determination of Fibrillarin Homologue From Hyperthermo... -

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Basic information

Entry
Database: PDB / ID: 1pry
TitleStructure Determination of Fibrillarin Homologue From Hyperthermophilic Archaeon Pyrococcus furiosus (Pfu-65527)
ComponentsFibrillarin-like pre-rRNA processing protein
KeywordsTRANSFERASE / Structural Genomics / Fibrillarin / Pyrococcus furiosus / snoRNP / ribosomal RNA processing / methylation / Pfu-65527 / PSI / Protein Structure Initiative / Southeast Collaboratory for Structural Genomics / SECSG
Function / homology
Function and homology information


tRNA processing / S-adenosylmethionine-dependent methyltransferase activity / Transferases; Transferring one-carbon groups; Methyltransferases / 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
Fibrillarin-like rRNA/tRNA 2'-O-methyltransferase
Similarity search - Component
Biological speciesPyrococcus furiosus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Single Anomalous Scattering / Resolution: 1.97 Å
AuthorsDeng, L. / Starostina, N.G. / Liu, Z.-J. / Rose, J.P. / Terns, R.M. / Terns, M.P. / Wang, B.-C. / Southeast Collaboratory for Structural Genomics (SECSG)
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2004
Title: Structure determination of fibrillarin from the hyperthermophilic archaeon Pyrococcus furiosus
Authors: Deng, L. / Starostina, N.G. / Liu, Z.-J. / Rose, J.P. / Terns, R.M. / Terns, M.P. / Wang, B.-C. / Southeast Collaboratory for Structural Genomics
History
DepositionJun 20, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 9, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 24, 2018Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.4Feb 14, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Fibrillarin-like pre-rRNA processing protein


Theoretical massNumber of molelcules
Total (without water)25,7851
Polymers25,7851
Non-polymers00
Water2,846158
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)43.967, 62.082, 103.363
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Fibrillarin-like pre-rRNA processing protein


Mass: 25784.809 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus furiosus (archaea) / Gene: FLPA OR PF0059 / Plasmid: pET-21b(+) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q8U4M2
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 158 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.74 Å3/Da / Density % sol: 55.03 %
Crystal growTemperature: 291 K / Method: microbatch / pH: 8.5
Details: PEG 6000, ammonium phosphate, pH 8.5, Microbatch, temperature 291K
Crystal grow
*PLUS
Temperature: 18 ℃ / Method: batch method
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
110 %PEG800011
2200 mMcalcium acetate11
3100 mMimidazole11pH8.0
412 %PEG600011
5100 mMdi-ammonium hydrogen phosphate11
6100 mMTris-HCl11pH8.5

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONAPS 17-ID11.74
SYNCHROTRONAPS 17-ID20.97
Detector
TypeIDDetectorDate
MARRESEARCH1CCDOct 16, 2001
MARRESEARCH2CCDNov 18, 2001
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2Mx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
11.741
20.971
ReflectionResolution: 1.97→40.46 Å / Num. all: 18879 / Num. obs: 18879 / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Rsym value: 0.052 / Net I/σ(I): 19.4
Reflection shellResolution: 1.97→2.05 Å / Rsym value: 0.378 / % possible all: 33.9
Reflection
*PLUS
% possible obs: 82.3 % / Rmerge(I) obs: 0.052

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: Single Anomalous Scattering / Resolution: 1.97→53.45 Å / SU B: 4.782 / SU ML: 0.129 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / ESU R: 0.213 / ESU R Free: 0.193 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.25909 1749 9.7 %RANDOM
Rwork0.20437 ---
obs0.2097 16201 86.78 %-
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 mean: 35.298 Å2
Baniso -1Baniso -2Baniso -3
1--0.64 Å20 Å20 Å2
2--0.48 Å20 Å2
3---0.16 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.34 Å0.28 Å
Luzzati d res low-5 Å
Luzzati sigma a0.27 Å0.23 Å
Refinement stepCycle: LAST / Resolution: 1.97→53.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1819 0 0 158 1977
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0221858
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.351.9692513
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0955225
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0970.2279
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021386
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1840.2829
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1290.2147
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2350.223
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1670.25
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it0.7441.51126
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.37421836
X-RAY DIFFRACTIONr_scbond_it2.0883732
X-RAY DIFFRACTIONr_scangle_it3.5354.5677
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.97→2.021 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.42 24
Rwork0.314 273
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAM
Refinement
*PLUS
Lowest resolution: 40.06 Å / Num. reflection obs: 17950 / σ(F): 2 / % reflection Rfree: 9.7 % / Rfactor obs: 0.228 / Rfactor Rfree: 0.272
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.006
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.3
X-RAY DIFFRACTIONr_dihedral_angle_d
X-RAY DIFFRACTIONr_dihedral_angle_deg23.9
X-RAY DIFFRACTIONr_improper_angle_d
X-RAY DIFFRACTIONr_improper_angle_deg0.79
LS refinement shell
*PLUS
Rfactor Rfree: 0.42 / Rfactor Rwork: 0.314

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