1NBS | pdb_00001nbs

Crystal structure of the specificity domain of Ribonuclease P RNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.15 Å
  • R-Value Free: 
    0.307 (Depositor), 0.308 (DCC) 
  • R-Value Work: 
    0.280 (Depositor), 0.286 (DCC) 
  • R-Value Observed: 
    0.282 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 1NBS

This is version 1.5 of the entry. See complete history

Literature

Crystal structure of the specificity domain of Ribonuclease P

Krasilnikov, A.S.Yang, X.Pan, T.Mondragon, A.

(2003) Nature 421: 760-764

  • DOI: https://doi.org/10.1038/nature01386
  • Primary Citation Related Structures: 
    1NBS

  • PubMed Abstract: 

    RNase P is the only endonuclease responsible for processing the 5' end of transfer RNA by cleaving a precursor and leading to tRNA maturation. It contains an RNA component and a protein component and has been identified in all organisms. It was one of the first catalytic RNAs identified and the first that acts as a multiple-turnover enzyme in vivo. RNase P and the ribosome are so far the only two ribozymes known to be conserved in all kingdoms of life. The RNA component of bacterial RNase P can catalyse pre-tRNA cleavage in the absence of the RNase P protein in vitro and consists of two domains: a specificity domain and a catalytic domain. Here we report a 3.15-A resolution crystal structure of the 154-nucleotide specificity domain of Bacillus subtilis RNase P. The structure reveals the architecture of this domain, the interactions that maintain the overall fold of the molecule, a large non-helical but well-structured module that is conserved in all RNase P RNA, and the regions that are involved in interactions with the substrate.


  • Organizational Affiliation
    • Department of Biochemistry, Molecular Biology and Cell Biology, Northwestern University, Evanston, Illinois 60208, USA.

Macromolecule Content 

  • Total Structure Weight: 105.48 kDa 
  • Atom Count: 5,837 
  • Modeled Residue Count: 270 
  • Deposited Residue Count: 310 
  • Unique nucleic acid chains: 1

Macromolecules

Find similar nucleic acids by:  (by identity cutoff) 
Entity ID: 1
MoleculeChains LengthOrganismImage
RIBONUCLEASE P RNA
A, B
155Bacillus subtilis
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PB

Query on PB



Download:Ideal Coordinates CCD File
AA [auth B]
BA [auth B]
CA [auth B]
DA [auth B]
EA [auth B]
AA [auth B],
BA [auth B],
CA [auth B],
DA [auth B],
EA [auth B],
FA [auth B],
GA [auth B],
H [auth A],
HA [auth B],
I [auth A],
IA [auth B],
J [auth A],
JA [auth B],
K [auth A],
KA [auth B],
L [auth A],
M [auth A],
N [auth A],
O [auth A],
P [auth A],
Q [auth A],
R [auth A],
S [auth A]
LEAD (II) ION
Pb
RVPVRDXYQKGNMQ-UHFFFAOYSA-N
MG

Query on MG



Download:Ideal Coordinates CCD File
C [auth A]
D [auth A]
E [auth A]
F [auth A]
G [auth A]
C [auth A],
D [auth A],
E [auth A],
F [auth A],
G [auth A],
T [auth B],
U [auth B],
V [auth B],
W [auth B],
X [auth B],
Y [auth B],
Z [auth B]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.15 Å
  • R-Value Free:  0.307 (Depositor), 0.308 (DCC) 
  • R-Value Work:  0.280 (Depositor), 0.286 (DCC) 
  • R-Value Observed: 0.282 (Depositor) 
Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 126.5α = 90
b = 145.3β = 90
c = 144.6γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
SCALAdata scaling
SHARPphasing
CNSrefinement
XDSdata scaling
XDSdata reduction
CCP4data scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2003-02-18
    Type: Initial release
  • Version 1.1: 2008-04-28
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2019-07-24
    Changes: Advisory, Data collection, Refinement description
  • Version 1.4: 2021-10-27
    Changes: Advisory, Database references, Derived calculations
  • Version 1.5: 2024-02-14
    Changes: Data collection