4K7M | pdb_00004k7m

Crystal structure of RNase S variant (K7C/Q11C) with bound mercury ions

• PDB DOI: https://doi.org/10.2210/pdb4K7M/pdb

• Classification: HYDROLASE
• Organism(s): Bos taurus
• Mutation(s): Yes 


• Deposited: 2013-04-17 Released: 2013-11-27 
• Deposition Author(s): Genz, M., Straeter, N.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.205 (Depositor), 0.200 (DCC) 
• R-Value Work: 
  0.165 (Depositor), 0.170 (DCC) 
• R-Value Observed: 
  0.167 (Depositor) 

Starting Model: experimental

Literature

Crystal Structure of Apo- and Metalated Thiolate containing RNase S as Structural Basis for the Design of Artificial Metalloenzymes by Peptide- Protein Complementation

Genz, M., Singer, D., Hey-Hawkins, E., Hoffmann, R., Straeter, N.

(2013) Z Anorg Allg Chem 639: 2395-2400

• DOI: https://doi.org/10.1002/zaac.201300410

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 13.83 kDa 
• Atom Count: 1,069 
• Modelled Residue Count: 118 
• Deposited Residue Count: 119 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribonuclease pancreatic	A	119	Bos taurus	Mutation(s): 2  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

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HG	B [auth A], C [auth A]	MERCURY (II) ION Hg BQPIGGFYSBELGY-UHFFFAOYSA-N
SO4	D [auth A], E [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.205 (Depositor), 0.200 (DCC) 
• R-Value Work:  0.165 (Depositor), 0.170 (DCC) 
• R-Value Observed: 0.167 (Depositor) 

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 43.87	α = 90
b = 43.87	β = 90
c = 96.361	γ = 120

Software Package:

Software Name	Purpose
MAR345dtb	data collection
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-11-27 
Deposition Author(s): Genz, M., Straeter, N.

Revision History  

• Version 1.0: 2013-11-27
  Type: Initial release
  
• Version 1.1: 2017-11-15
  Changes: Refinement description
• Version 1.2: 2018-08-29
  Changes: Data collection, Database references, Source and taxonomy, Structure summary
• Version 1.3: 2023-09-20
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.4: 2024-10-09
  Changes: Structure summary