1ZGX | pdb_00001zgx

Crystal structure of ribonuclease mutant

• PDB DOI: https://doi.org/10.2210/pdb1ZGX/pdb

• Classification: HYDROLASE
• Organism(s): Kitasatospora aureofaciens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2005-04-22 Released: 2006-08-08 
• Deposition Author(s): Urbanikova, L., Sevcik, J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.13 Å
• R-Value Free: 
  0.164 (Depositor), 0.187 (DCC) 
• R-Value Work: 
  0.128 (Depositor) 
• R-Value Observed: 
  0.129 (Depositor) 

Starting Model: experimental

Literature

Surface mutation Gln to Lys changed the crystal packing

Urbanikova, L., Sevcik, J.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 10.89 kDa 
• Atom Count: 1,004 
• Modeled Residue Count: 96 
• Deposited Residue Count: 96 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Guanyl-specific ribonuclease Sa	A	63	Kitasatospora aureofaciens	Mutation(s): 0  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 ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Guanyl-specific ribonuclease Sa	B	33	Kitasatospora aureofaciens	Mutation(s): 1  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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	C [auth A], D [auth B], E [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.13 Å
• R-Value Free:  0.164 (Depositor), 0.187 (DCC) 
• R-Value Work:  0.128 (Depositor) 
• R-Value Observed: 0.129 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 34.582	α = 90
b = 41.513	β = 90
c = 58.403	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-08-08 
Deposition Author(s): Urbanikova, L., Sevcik, J.

Revision History  

• Version 1.0: 2006-08-08
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2021-10-20
  Changes: Data collection, Database references, Derived calculations
• Version 1.4: 2023-08-23
  Changes: Data collection, Refinement description
• Version 1.5: 2024-10-30
  Changes: Structure summary