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- PDB-1nt2: CRYSTAL STRUCTURE OF FIBRILLARIN/NOP5P COMPLEX -

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Basic information

Entry
Database: PDB / ID: 1nt2
TitleCRYSTAL STRUCTURE OF FIBRILLARIN/NOP5P COMPLEX
Components
  • Fibrillarin-like pre-rRNA processing protein
  • conserved hypothetical protein
KeywordsRNA BINDING PROTEIN / AdeMet / binding motif
Function / homology
Function and homology information


tRNA processing / Transferases; Transferring one-carbon groups; Methyltransferases / methyltransferase activity / rRNA processing / methylation / RNA binding
Similarity search - Function
S-adenosyl-L-methionine-dependent methyltransferases / Fibrillarin homologue / Nop domain / Helix hairpin bin / Helix hairpin bin domain superfamily / rRNA 2'-O-methyltransferase fibrillarin-like / Fibrillarin, conserved site / Fibrillarin / Fibrillarin signature. / Fibrillarin ...S-adenosyl-L-methionine-dependent methyltransferases / Fibrillarin homologue / Nop domain / Helix hairpin bin / Helix hairpin bin domain superfamily / rRNA 2'-O-methyltransferase fibrillarin-like / Fibrillarin, conserved site / Fibrillarin / Fibrillarin signature. / Fibrillarin / Nop domain / Nop domain superfamily / Nop, C-terminal domain / snoRNA binding domain, fibrillarin / Nop domain profile. / Serum Albumin; Chain A, Domain 1 / Vaccinia Virus protein VP39 / Helix Hairpins / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold / 2-Layer Sandwich / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
S-ADENOSYLMETHIONINE / Nop domain-containing protein / Fibrillarin-like rRNA/tRNA 2'-O-methyltransferase
Similarity search - Component
Biological speciesArchaeoglobus fulgidus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.9 Å
AuthorsAittaleb, M. / Rashid, R. / Chen, Q. / Palmer, J.R. / Daniels, C.J. / Li, H.
CitationJournal: Nat.Struct.Biol. / Year: 2003
Title: Structure and function of archaeal box C/D sRNP core proteins.
Authors: Aittaleb, M. / Rashid, R. / Chen, Q. / Palmer, J.R. / Daniels, C.J. / Li, H.
History
DepositionJan 28, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 1, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Source and taxonomy / Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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
B: conserved hypothetical protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,8573
Polymers54,4592
Non-polymers3981
Water0
1
A: Fibrillarin-like pre-rRNA processing protein
B: conserved hypothetical protein
hetero molecules

A: Fibrillarin-like pre-rRNA processing protein
B: conserved hypothetical protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,7146
Polymers108,9174
Non-polymers7972
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_666-y+1,-x+1,-z+11
Buried area8310 Å2
ΔGint-55 kcal/mol
Surface area39410 Å2
MethodPISA
2
A: Fibrillarin-like pre-rRNA processing protein
B: conserved hypothetical protein
hetero molecules

A: Fibrillarin-like pre-rRNA processing protein
B: conserved hypothetical protein
hetero molecules

A: Fibrillarin-like pre-rRNA processing protein
B: conserved hypothetical protein
hetero molecules

A: Fibrillarin-like pre-rRNA processing protein
B: conserved hypothetical protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)219,42812
Polymers217,8358
Non-polymers1,5944
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
crystal symmetry operation7_556y,x,-z+11
crystal symmetry operation8_666-y+1,-x+1,-z+11
MethodPQS
Unit cell
Length a, b, c (Å)125.308, 125.308, 87.482
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Space group name H-MP42212
Detailsa homodimer of two asu heterodimers is generated by the two-fold along the cell diagonal: 1-Y, 1-X, 1-Z

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Components

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


Mass: 24366.293 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Archaeoglobus fulgidus (archaea) / Strain: DSM4304 / Gene: flpA / Plasmid: pET13b / Production host: Escherichia coli (E. coli) / Strain (production host): BLR21(DE3) / References: UniProt: O28192
#2: Protein conserved hypothetical protein


Mass: 30092.379 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Archaeoglobus fulgidus (archaea) / Strain: DSM4304 / Gene: AF2088 / Plasmid: pBR / Production host: Escherichia coli (E. coli) / References: UniProt: O28191
#3: Chemical ChemComp-SAM / S-ADENOSYLMETHIONINE / S-Adenosyl methionine


Mass: 398.437 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H22N6O5S

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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: 3.34 Å3/Da / Density % sol: 62.92 %
Crystal growTemperature: 295 K / Method: vapor diffusion / pH: 8.6 / Details: PEG, pH 8.6, VAPOR DIFFUSION, temperature 295K
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
1100 mMTris-HCl1reservoirpH8.6
2200 mMtrisodium citrate1reservoir
335-40 %(w/v)PEG4001reservoir
420-30 mg/molprotein1drop

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONAPS 14-BM-C11
SYNCHROTRONNSLS X4A20.97
Detector
TypeIDDetector
ADSC QUANTUM 41CCD
ADSC QUANTUM 42CCD
RadiationMonochromator: Si 111 Channel / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
111
20.971
ReflectionResolution: 2.9→50 Å / Num. all: 15869 / Num. obs: 12451 / % possible obs: 78.5 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 4.7 % / Biso Wilson estimate: 42.2 Å2 / Rmerge(I) obs: 0.094 / Rsym value: 0.094 / Net I/σ(I): 11.7
Reflection shellResolution: 2.9→2.97 Å / Redundancy: 1.5 % / Rmerge(I) obs: 0.31 / Mean I/σ(I) obs: 1.3 / Num. unique all: 1014 / Rsym value: 0.31 / % possible all: 25.5
Reflection
*PLUS
Highest resolution: 2.9 Å / Lowest resolution: 50 Å / Num. measured all: 75425 / Rmerge(I) obs: 0.122
Reflection shell
*PLUS
% possible obs: 20.5 % / Rmerge(I) obs: 0.4

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Processing

Software
NameClassification
CAD4data collection
DENZOdata reduction
CNSrefinement
CAD4data reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MAD / Resolution: 2.9→31.33 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 244888.64 / Data cutoff high rms absF: 244888.64 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.323 1209 10.2 %RANDOM
Rwork0.257 ---
all0.257 11841 --
obs0.257 11841 74.2 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 17.5356 Å2 / ksol: 0.33134 e/Å3
Displacement parametersBiso mean: 47.9 Å2
Baniso -1Baniso -2Baniso -3
1-9.68 Å20 Å20 Å2
2--9.68 Å20 Å2
3----19.35 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.67 Å0.53 Å
Luzzati d res low-5 Å
Luzzati sigma a0.95 Å0.9 Å
Refinement stepCycle: LAST / Resolution: 2.9→31.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3641 0 27 0 3668
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d21.9
X-RAY DIFFRACTIONc_improper_angle_d0.83
LS refinement shellResolution: 2.9→3.08 Å / Rfactor Rfree error: 0.052 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.447 73 13.5 %
Rwork0.451 469 -
obs--21 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2SAM.PAR
Refinement
*PLUS
Highest resolution: 2.9 Å / Lowest resolution: 50 Å / % reflection Rfree: 10 % / Rfactor Rfree: 0.316 / Rfactor Rwork: 0.254
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.39
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg21.9
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.83

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