1LNI | pdb_00001lni

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 Work: 
    0.125 (DCC) 
  • R-Value Observed: 
    0.116 (Depositor) 

Starting Model: experimental
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This is version 1.5 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: https://doi.org/10.1107/s0907444902010090
  • Primary Citation 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'-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

Macromolecule Content 

  • Total Structure Weight: 21.54 kDa 
  • Atom Count: 2,301 
  • Modeled Residue Count: 192 
  • Deposited Residue Count: 192 
  • Unique protein chains: 1

Macromolecules

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|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
GUANYL-SPECIFIC RIBONUCLEASE SA
A, B
96Kitasatospora aureofaciensMutation(s): 0 
Gene Names: U39467
EC: 3.1.27.3 (PDB Primary Data), 4.6.1.24 (UniProt)
UniProt
Find proteins for P05798 (Kitasatospora aureofaciens)
Explore P05798 
Go to UniProtKB:  P05798
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP05798
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.00 Å
  • R-Value Work:  0.125 (DCC) 
  • R-Value Observed: 0.116 (Depositor) 
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  (Full details and data files)

  • 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
  • Version 1.4: 2023-08-16
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 1.5: 2024-11-13
    Changes: Structure summary