3OQY

Semi-synthetic ribonuclease S: para-cyano-phenylalanine at position 8


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.49 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.202 
  • R-Value Observed: 0.203 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Nitrile bonds as infrared probes of electrostatics in ribonuclease S.

Fafarman, A.T.Boxer, S.G.

(2010) J Phys Chem B 114: 13536-13544

  • DOI: 10.1021/jp106406p
  • Primary Citation of Related Structures:  
    3OQY, 3OQZ, 3OR0

  • PubMed Abstract: 
  • Three different nitrile-containing amino acids, p-cyanophenylalanine, m-cyanophenylalanine, and S-cyanohomocysteine, have been introduced near the active site of the semisynthetic enzyme ribonuclease S (RNase S) to serve as probes of electrostatic fields ...

    Three different nitrile-containing amino acids, p-cyanophenylalanine, m-cyanophenylalanine, and S-cyanohomocysteine, have been introduced near the active site of the semisynthetic enzyme ribonuclease S (RNase S) to serve as probes of electrostatic fields. Vibrational Stark spectra, measured directly on the probe-modified proteins, confirm the predominance of the linear Stark tuning rate in describing the sensitivity of the nitrile stretch to external electric fields, a necessary property for interpreting observed frequency shifts as a quantitative measure of local electric fields that can be compared with simulations. The X-ray structures of these nitrile-modified RNase variants and enzymatic assays demonstrate minimal perturbation to the structure and function, respectively, by the probes and provide a context for understanding the influence of the environment on the nitrile stretching frequency. We examine the ability of simulation techniques to recapitulate the spectroscopic properties of these nitriles as a means to directly test a computational electrostatic model for proteins, specifically that in the ubiquitous Amber-99 force field. Although qualitative agreement between theory and experiment is observed for the largest shifts, substantial discrepancies are observed in some cases, highlighting the ongoing need for experimental metrics to inform the development of theoretical models of electrostatic fields in proteins.


    Organizational Affiliation

    Department of Chemistry, Stanford University, Stanford, California 94305-5080, USA.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Ribonuclease pancreaticC [auth a],
A [auth b]
15Bos taurusMutation(s): 0 
Gene Names: RNASE1RNS1
EC: 3.1.27.5 (PDB Primary Data), 4.6.1.18 (UniProt)
UniProt
Find proteins for P61823 (Bos taurus)
Explore P61823 
Go to UniProtKB:  P61823
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP61823
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Ribonuclease pancreaticD [auth A],
B
104Bos taurusMutation(s): 0 
Gene Names: RNASE1RNS1
EC: 3.1.27.5 (PDB Primary Data), 4.6.1.18 (UniProt)
UniProt
Find proteins for P61823 (Bos taurus)
Explore P61823 
Go to UniProtKB:  P61823
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP61823
Protein Feature View
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  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
4CF
Query on 4CF
A [auth b],
C [auth a]
L-PEPTIDE LINKINGC10 H10 N2 O2PHE
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.49 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.202 
  • R-Value Observed: 0.203 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 100.906α = 90
b = 32.52β = 91.01
c = 68.932γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
CNSrefinement
HKL-2000data collection
DENZOdata reduction
SCALAdata scaling
CNSphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-10-20
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2019-07-17
    Changes: Data collection, Derived calculations, Refinement description