- PDB-2jnb: Solution Structure of RNA-binding protein 15.5K -
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Open data
ID or keywords:
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Basic information
Entry
Database: PDB / ID: 2jnb
Title
Solution Structure of RNA-binding protein 15.5K
Components
NHP2-like protein 1
Keywords
RNA BINDING PROTEIN / splicing / kink-turn RNA-binding protein / nhpx
Function / homology
Function and homology information
U4atac snRNP / U4atac snRNA binding / box C/D sno(s)RNA binding / dense fibrillar component / U4 snRNA binding / box C/D methylation guide snoRNP complex / U2-type precatalytic spliceosome / box C/D snoRNP assembly / rRNA modification in the nucleus and cytosol / U3 snoRNA binding ...U4atac snRNP / U4atac snRNA binding / box C/D sno(s)RNA binding / dense fibrillar component / U4 snRNA binding / box C/D methylation guide snoRNP complex / U2-type precatalytic spliceosome / box C/D snoRNP assembly / rRNA modification in the nucleus and cytosol / U3 snoRNA binding / precatalytic spliceosome / single fertilization / Major pathway of rRNA processing in the nucleolus and cytosol / U4/U6 x U5 tri-snRNP complex / mRNA Splicing - Major Pathway / maturation of SSU-rRNA / small-subunit processome / mRNA splicing, via spliceosome / ribosomal small subunit biogenesis / ATPase binding / nucleolus / protein-containing complex / RNA binding / nucleoplasm / nucleus Similarity search - Function
H/ACA ribonucleoprotein complex, subunit Nhp2-like / Ribosomal protein L30/S12 / 60s Ribosomal Protein L30; Chain: A; / Ribosomal protein L7Ae conserved site / Ribosomal protein L7Ae signature. / : / Ribosomal protein L7Ae/L8/Nhp2 family / Ribosomal protein L7Ae/L30e/S12e/Gadd45 / Ribosomal protein L7Ae/L30e/S12e/Gadd45 family / 50S ribosomal protein L30e-like ...H/ACA ribonucleoprotein complex, subunit Nhp2-like / Ribosomal protein L30/S12 / 60s Ribosomal Protein L30; Chain: A; / Ribosomal protein L7Ae conserved site / Ribosomal protein L7Ae signature. / : / Ribosomal protein L7Ae/L8/Nhp2 family / Ribosomal protein L7Ae/L30e/S12e/Gadd45 / Ribosomal protein L7Ae/L30e/S12e/Gadd45 family / 50S ribosomal protein L30e-like / 2-Layer Sandwich / Alpha Beta Similarity search - Domain/homology
0.1 % sodium azide, 200 mM sodium chloride, 50 mM sodium phosphate, 0.9 mM [U-98% 13C, U-98% 15N] protein, 90% H2O, 10% D2O
90% H2O/10% D2O
Sample
Conc. (mg/ml)
Component
Isotopic labeling
Solution-ID
0.1 %
sodiumazide
1
100mM
sodiumchloride
1
100mM
sodiumphosphate
1
1.6mM
entity
1
0.1 %
sodiumazide
2
200mM
sodiumchloride
2
50mM
sodiumphosphate
2
.9mM
entity
[U-98% 13C; U-98% 15N]
2
Sample conditions
Conditions-ID
Ionic strength
pH
Pressure (kPa)
Temperature (K)
1
250
6
ambient
293K
2
200
6
ambient
293K
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NMR measurement
Radiation
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelength
Relative weight: 1
NMR spectrometer
Type
Manufacturer
Model
Field strength (MHz)
Spectrometer-ID
Varian INOVA
Varian
INOVA
600
1
Varian INOVA
Varian
INOVA
800
2
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Processing
NMR software
Name
Version
Developer
Classification
Felix
97
AccelrysSoftwareInc.
processing
Sparky
3.111
Goddard
chemicalshiftassignment
Sparky
3.111
Goddard
peakpicking
TALOS
Cornilescu, DelaglioandBax
dataanalysis
CYANA
2.1
Guntert, MumenthalerandWuthrich
structuresolution
ProcheckNMR
LaskowskiandMacArthur
dataanalysis
CYANA
2.1
Guntert, MumenthalerandWuthrich
refinement
Refinement
Method: simulated annealing / Software ordinal: 1
NMR constraints
NOE constraints total: 1090 / NOE long range total count: 229 / NOE medium range total count: 148 / Protein chi angle constraints total count: 0 / Protein other angle constraints total count: 0 / Protein phi angle constraints total count: 100 / Protein psi angle constraints total count: 100
NMR representative
Selection criteria: fewest violations
NMR ensemble
Conformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20 / Maximum lower distance constraint violation: 0.35 Å / Maximum upper distance constraint violation: 0.25 Å
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