3H8S | pdb_00003h8s

Structure of D19N T4 RNase H in the presence of divalent magnesium

• PDB DOI: https://doi.org/10.2210/pdb3H8S/pdb

• Classification: HYDROLASE
• Organism(s): Tequatrovirus T4
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2009-04-29 Released: 2010-05-12 
• Deposition Author(s): Tomanicek, S.J., Mueser, T.C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.51 Å
• R-Value Free: 
  0.234 (Depositor), 0.230 (DCC) 
• R-Value Work: 
  0.190 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.192 (Depositor) 

Starting Model: experimental

Literature

Additional Order Appears in the Absence of Metals in a FEN-1 protein: Structural Analysis of Magnesium Binding to Bacteriophage T4 RNaseH

Tomanicek, S.J., Devos, J.M., Mueser, T.C.

To be published.

Biological Assembly 1  

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

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

Macromolecule Content 

• Total Structure Weight: 35.63 kDa 
• Atom Count: 2,393 
• Modeled Residue Count: 284 
• Deposited Residue Count: 305 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribonuclease H	A	305	Tequatrovirus T4	Mutation(s): 1  Gene Names: 33.2, das, rnh EC: 3.1.26.4
UniProt
Find proteins for P13319 (Enterobacteria phage T4) Explore P13319  Go to UniProtKB:  P13319

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MG	B [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.51 Å
• R-Value Free:  0.234 (Depositor), 0.230 (DCC) 
• R-Value Work:  0.190 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.192 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 53.312	α = 90
b = 75.298	β = 90
c = 88.09	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-05-12 
Deposition Author(s): Tomanicek, S.J., Mueser, T.C.

Revision History  

• Version 1.0: 2010-05-12
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-11-01
  Changes: Refinement description
• Version 1.3: 2021-10-13
  Changes: Database references, Derived calculations
• Version 1.4: 2023-09-06
  Changes: Data collection, Refinement description