1LNI

CRYSTAL STRUCTURE ANALYSIS OF A RIBONUCLEASE FROM STREPTOMYCES AUREOFACIENS AT ATOMIC RESOLUTION (1.0 A)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.00 Å
  • R-Value Observed: 0.116 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Atomic resolution data reveal flexibility in the structure of RNase Sa.

Sevcik, J.Lamzin, V.S.Dauter, Z.Wilson, K.S.

(2002) Acta Crystallogr D Biol Crystallogr 58: 1307-1313

  • DOI: 10.1107/s0907444902010090
  • Primary Citation of Related Structures:  
    1LNI

  • PubMed Abstract: 
  • Ribonuclease from Streptomyces aureofaciens, the bacterial source for the industrial production of chlorotetracycline, is a guanylate endoribonuclease (RNase Sa; EC 3.1.27.3) which hydrolyses the phosphodiester bonds of single-stranded RNA at the 3'- ...

    Ribonuclease from Streptomyces aureofaciens, the bacterial source for the industrial production of chlorotetracycline, is a guanylate endoribonuclease (RNase Sa; EC 3.1.27.3) which hydrolyses the phosphodiester bonds of single-stranded RNA at the 3'-side of guanosine nucleotides with high specificity. The structure of the enzyme was previously refined at atomic resolution (1.2 A) using room-temperature data. Here, the RNase Sa structure refined against 1.0 A data collected at cryogenic temperature is reported. There are two surface loops in molecule A and one in molecule B for which two main-chain conformations are modelled: these loops contain active-site residues. The separation for most of the corresponding main-chain atoms in the two conformations is about 0.8 A, with a maximum of 2.5 A. The two regions of dual conformation represent the most important differences in comparison with the structure determined at room temperature, where the corresponding loops have one conformation only but the largest degree of anisotropy. The flexibility of the loops observed in the structure of RNase Sa is directly linked to the need for the active site to interact productively with substrates and/or inhibitors.


    Organizational Affiliation

    Institute of Molecular Biology, Slovak Academy of Sciences, Bratislava, Slovak Republic. umbisevc@savba.savba.sk



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
GUANYL-SPECIFIC RIBONUCLEASE SAAB96Kitasatospora aureofaciensMutation(s): 0 
Gene Names: U39467rnaSA
EC: 3.1.27.3 (PDB Primary Data), 4.6.1.24 (UniProt)
Find proteins for P05798 (Kitasatospora aureofaciens)
Explore P05798 
Go to UniProtKB:  P05798
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GOL
Query on GOL

Download CCD File 
A, B
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.00 Å
  • R-Value Observed: 0.116 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 64.2α = 90
b = 77.8β = 90
c = 38.28γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
Startingmodel building
SHELXLrefinement
STARTINGphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2002-07-31
    Type: Initial release
  • Version 1.1: 2008-04-28
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Non-polymer description, Version format compliance
  • Version 1.3: 2017-10-11
    Changes: Refinement description