3H8S

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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.51 Å
R-Value Free: 0.234
R-Value Work: 0.190
R-Value Observed: 0.192

wwPDB Validation 3D Report Full Report

This is version 1.4 of the entry. See complete history.

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.

Macromolecule Content

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

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P13319
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A]	B [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.51 Å
R-Value Free: 0.234
R-Value Work: 0.190
R-Value Observed: 0.192
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

View Full Validation Report

Entry History

Deposition Data

Released Date: 2010-05-12

Deposition Author(s):

Tomanicek, S.J.

Revision History (Full details and data files)

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

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.