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- PDB-1g8a: PYROCOCCUS HORIKOSHII FIBRILLARIN PRE-RRNA PROCESSING PROTEIN -

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Basic information

Entry
Database: PDB / ID: 1g8a
TitlePYROCOCCUS HORIKOSHII FIBRILLARIN PRE-RRNA PROCESSING PROTEIN
ComponentsFIBRILLARIN-LIKE PRE-RRNA PROCESSING PROTEIN
KeywordsRNA BINDING PROTEIN / rRNA binding / RNA binding / Structural Genomics / BSGC structure funded by NIH / Protein Structure Initiative / PSI / Berkeley Structural Genomics Center
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
Fibrillarin-like rRNA/tRNA 2'-O-methyltransferase
Similarity search - Component
Biological speciesPyrococcus horikoshii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsBoisvert, D.C. / Kim, S.H. / Berkeley Structural Genomics Center (BSGC)
CitationJournal: To be Published
Title: A Structural Approach to Gene Function and Structure Quality for Pyrococcus horikoshii Fibrillarin
Authors: Boisvert, D.C. / Kim, S.H.
History
DepositionNov 16, 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
Revision 1.4Jan 31, 2018Group: Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 1.5Aug 9, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)25,8651
Polymers25,8651
Non-polymers00
Water7,332407
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)46.376, 41.098, 54.168
Angle α, β, γ (deg.)90.00, 98.26, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 25864.746 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus horikoshii (archaea) / Gene: 0048 / Plasmid: PET21A / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O57811
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 407 / 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: 1.97 Å3/Da / Density % sol: 37.69 %
Crystal growTemperature: 277 K / Method: cooling / pH: 7.5
Details: 50 mM NaCl, 50 mM Tris, 85 mg/ml fibrillarin, pH 7.5, Cooling, temperature 4K

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Data collection

DiffractionMean temperature: 180 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 0.95 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 4, 2000
RadiationMonochromator: Standard at ALS 5.0.2 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95 Å / Relative weight: 1
ReflectionResolution: 1.4→40 Å / Num. all: 43002 / Num. obs: 37696 / % possible obs: 94.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3 % / Biso Wilson estimate: 10.9 Å2 / Rmerge(I) obs: 0.033 / Net I/σ(I): 40
Reflection shellResolution: 1.4→1.49 Å / Redundancy: 2 % / Rmerge(I) obs: 0.06 / % possible all: 71.2

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Processing

Software
NameVersionClassification
Adxvdata processing
DENZOSUITEdata reduction
SCALEPACKSUITEdata scaling
EPMRphasing
CNS1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1FIB

1fib


Resolution: 1.4→40 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 471722.3 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: MLF
RfactorNum. reflection% reflectionSelection details
Rfree0.218 1879 5 %RANDOM
Rwork0.203 ---
all0.203 43002 --
obs0.203 37696 94.2 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 38.17 Å2 / ksol: 0.339 e/Å3
Displacement parametersBiso mean: 13.8 Å2
Baniso -1Baniso -2Baniso -3
1-0.37 Å20 Å20.65 Å2
2---0.02 Å20 Å2
3----0.35 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.18 Å0.16 Å
Luzzati d res low-5 Å
Luzzati sigma a0.07 Å0.06 Å
Refinement stepCycle: LAST / Resolution: 1.4→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1825 0 0 407 2232
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d24.3
X-RAY DIFFRACTIONc_improper_angle_d0.85
X-RAY DIFFRACTIONc_mcbond_it1.131.5
X-RAY DIFFRACTIONc_mcangle_it1.742
X-RAY DIFFRACTIONc_scbond_it2.552
X-RAY DIFFRACTIONc_scangle_it3.452.5
LS refinement shellResolution: 1.4→1.49 Å / Rfactor Rfree error: 0.016 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.252 260 5.5 %
Rwork0.22 4453 -
obs-4713 71 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP

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