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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 / homologyHelix hairpin bin domain superfamily / Fibrillarin / Nop domain profile. / Fibrillarin signature. / Fibrillarin / Nop domain / Fibrillarin, conserved site / snoRNA binding domain, fibrillarin / S-adenosyl-L-methionine-dependent methyltransferase / Nop domain superfamily ...Helix hairpin bin domain superfamily / Fibrillarin / Nop domain profile. / Fibrillarin signature. / Fibrillarin / Nop domain / Fibrillarin, conserved site / snoRNA binding domain, fibrillarin / S-adenosyl-L-methionine-dependent methyltransferase / Nop domain superfamily / tRNA processing / Methyltransferases / methyltransferase activity / rRNA processing / RNA binding / Uncharacterized protein / Fibrillarin-like rRNA/tRNA 2'-O-methyltransferase
Function and homology information
Specimen sourceArchaeoglobus fulgidus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / 2.9 Å resolution
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.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Jan 28, 2003 / Release: Apr 1, 2003
RevisionDateData content typeGroupProviderType
1.0Apr 1, 2003Structure modelrepositoryInitial release
1.1Apr 29, 2008Structure modelVersion format compliance
1.2Jul 13, 2011Structure modelDerived calculations / Source and taxonomy / Version format compliance

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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
Polyers54,4592
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
Polyers108,9174
Non-polymers7972
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_666-y+1,-x+1,-z+11
Buried area (Å2)8310
ΔGint (kcal/M)-55
Surface area (Å2)39410
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
Polyers217,8358
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
γ
α
β
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-MP 42 21 2
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/peptide Fibrillarin-like pre-rRNA processing protein


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


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


Mass: 398.437 Da / Num. of mol.: 1 / Formula: C15H22N6O5S / S-Adenosyl methionine

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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 / Density percent sol: 62.92 %
Crystal growTemp: 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
IDConcCommon 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 temperatureCrystal ID
11001
21
Source
SourceTypeSynchrotron siteBeamlineIdWavelength
SYNCHROTRONAPS BEAMLINE 14-BM-CAPS14-BM-C11.0
SYNCHROTRONNSLS BEAMLINE X4ANSLSX4A20.97
Detector
TypeIdDetector
ADSC QUANTUM 41CCD
ADSC QUANTUM 42CCD
RadiationMonochromator: Si 111 Channel / Diffraction protocol: MAD / Monochromatic or laue m l: M / Scattering type: x-ray
Radiation wavelength
IDWavelengthRelative weight
11.01.0
20.971.0
ReflectionB iso Wilson estimate: 42.2 Å2 / D resolution high: 2.9 Å / D resolution low: 5 Å / Number all: 15869 / Number obs: 12451 / Observed criterion sigma F: 2 / Observed criterion sigma I: 2 / Rmerge I obs: 0.094 / Rsym value: 0.094 / NetI over sigmaI: 11.7 / Redundancy: 4.7 % / Percent possible obs: 78.5
Reflection shellRmerge I obs: 0.31 / Highest resolution: 2.9 Å / Lowest resolution: 2.97 Å / MeanI over sigI obs: 1.3 / Number unique all: 1014 / Rsym value: 0.31 / Redundancy: 1.5 % / Percent possible all: 25.5
Reflection
*PLUS
D resolution high: 2.9 Å / D resolution low: 5 Å / Number measured all: 75425 / Rmerge I obs: 0.122
Reflection shell
*PLUS
Percent 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
RefineMethod to determine structure: MAD / R Free selection details: RANDOM / 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 / Sigma F: 0 / Sigma I: 0 / Stereochemistry target values: Engh & Huber
Solvent computationSolvent model details: FLAT MODEL / Solvent model param bsol: 17.5356 / Solvent model param ksol: 0.33134
Displacement parametersB iso mean: 47.9 Å2 / Aniso B11: 9.68 Å2 / Aniso B12: 0 Å2 / Aniso B13: 0 Å2 / Aniso B22: 9.68 Å2 / Aniso B23: 0 Å2 / Aniso B33: -19.35 Å2
Least-squares processR factor R free: 0.323 / R factor R free error: 0.009 / R factor R work: 0.257 / R factor all: 0.257 / R factor obs: 0.257 / Highest resolution: 2.9 Å / Lowest resolution: 31.33 Å / Number reflection R free: 1209 / Number reflection all: 11841 / Number reflection obs: 11841 / Percent reflection R free: 10.2 / Percent reflection obs: 74.2
Refine analyzeLuzzati coordinate error free: 0.67 Å / Luzzati coordinate error obs: 0.53 Å / Luzzati d res low obs: 5 Å / Luzzati sigma a free: 0.95 Å / Luzzati sigma a obs: 0.9 Å
Refine hist #LASTHighest resolution: 2.9 Å / Lowest resolution: 31.33 Å
Number of atoms included #LASTProtein: 3641 / Nucleic acid: 0 / Ligand: 27 / Solvent: 0 / Total: 3668
Refine LS restraints
Refine IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.30
X-RAY DIFFRACTIONc_dihedral_angle_d21.90
X-RAY DIFFRACTIONc_improper_angle_d0.83
Refine LS shellHighest resolution: 2.9 Å / R factor R free: 0.447 / R factor R free error: 0.052 / R factor R work: 0.451 / Lowest resolution: 3.08 Å / Number reflection R free: 73 / Number reflection R work: 469 / Total number of bins used: 6 / Percent reflection R free: 13.5 / Percent reflection obs: 21
Xplor file
Refine IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2SAM.PAR
Least-squares process
*PLUS
R factor R free: 0.316 / R factor R work: 0.254 / Highest resolution: 2.9 Å / Lowest resolution: 5 Å / Percent reflection R free: 1
Refine LS restraints
*PLUS
Refine IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.39
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg21.90
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.83

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