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- PDB-1g8s: METHANOCOCCUS JANNASCHII FIBRILLARIN PRE-RRNA PROCESSING PROTEIN -

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Basic information

Entry
Database: PDB / ID: 1g8s
TitleMETHANOCOCCUS JANNASCHII FIBRILLARIN PRE-RRNA PROCESSING PROTEIN
ComponentsFIBRILLARIN-LIKE PRE-RRNA PROCESSING PROTEIN
KeywordsRNA BINDING PROTEIN / rRNA processing / RNA binding
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
METHIONINE / Fibrillarin-like rRNA/tRNA 2'-O-methyltransferase
Similarity search - Component
Biological speciesMethanocaldococcus jannaschii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.6 Å
AuthorsBoisvert, D.C. / Kim, S.H.
Citation
Journal: To be Published
Title: A Structural Approach to Gene Function and Structure Quality for Pyrococcus horikshii Fibrillarin
Authors: Boisvert, D.C. / Kim, S.H.
#1: Journal: Embo J. / Year: 2000
Title: Crystal structure of a fibrillarin homologue from Methanococcus jannaschii, a hyperthermophile, at 1.6 angstroms resolution
Authors: Wang, H. / Bosivert, D.C. / Kim, K.K. / Kim, R. / Kim, S.H.
History
DepositionNov 20, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 14, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.name / _software.version
Revision 1.4Aug 9, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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 PRE-RRNA PROCESSING PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,1542
Polymers26,0051
Non-polymers1491
Water2,522140
1
A: FIBRILLARIN-LIKE PRE-RRNA PROCESSING PROTEIN
hetero molecules

A: FIBRILLARIN-LIKE PRE-RRNA PROCESSING PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,3094
Polymers52,0112
Non-polymers2982
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Unit cell
Length a, b, c (Å)121.152, 43.212, 55.197
Angle α, β, γ (deg.)90.00, 96.98, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein FIBRILLARIN-LIKE PRE-RRNA PROCESSING PROTEIN


Mass: 26005.258 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanocaldococcus jannaschii (archaea)
Gene: 0697 / Plasmid: PET21A / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3) / References: UniProt: Q58108
#2: Chemical ChemComp-MET / METHIONINE


Type: L-peptide linking / Mass: 149.211 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H11NO2S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 140 / 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: 2.76 Å3/Da / Density % sol: 55.38 %
Crystal growTemperature: 273 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 20% PEG 4000, 20% Isopropanol, 0.1 M NaCitrate, 25 mg/ml fibrillarin, pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 273K

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Data collection

DiffractionMean temperature: 170 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.97894 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Oct 1, 1997 / Details: monochromatic
RadiationMonochromator: monochromatic / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97894 Å / Relative weight: 1
ReflectionResolution: 1.6→40 Å / Num. all: 71996 / Num. obs: 68772 / % possible obs: 97 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2 % / Biso Wilson estimate: 22.8 Å2 / Rmerge(I) obs: 0.076
Reflection shellResolution: 1.6→1.7 Å / Redundancy: 2 % / Rmerge(I) obs: 0.4 / % possible all: 95.8

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Processing

Software
NameVersionClassification
DENZOSUITEdata reduction
SCALEPACKSUITEdata scaling
CNS1refinement
RefinementMethod to determine structure: MAD
Starting model: 1FBN

1fbn


Resolution: 1.6→40 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 966006.53 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0.001 / σ(I): 0.001
Details: Probe program was used to identify residues incorrectly refined by CNS
RfactorNum. reflection% reflectionSelection details
Rfree0.213 3409 5 %RANDOM
Rwork0.201 ---
all0.202 71996 --
obs0.2016 68772 93.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 55.73 Å2 / ksol: 0.377 e/Å3
Displacement parametersBiso mean: 27.8 Å2
Baniso -1Baniso -2Baniso -3
1--4.57 Å20 Å2-3.37 Å2
2--4.8 Å20 Å2
3----0.22 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.22 Å0.2 Å
Luzzati d res low-5 Å
Luzzati sigma a0.23 Å0.22 Å
Refinement stepCycle: LAST / Resolution: 1.6→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1829 0 9 140 1978
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
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_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d25.1
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.78
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.891.5
X-RAY DIFFRACTIONc_mcangle_it2.952
X-RAY DIFFRACTIONc_scbond_it3.412
X-RAY DIFFRACTIONc_scangle_it5.282.5
LS refinement shellResolution: 1.6→1.7 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.311 465 4.6 %
Rwork0.309 9632 -
obs-10097 83 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP

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