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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.51 Å
R-Value Free:
0.234 (Depositor), 0.241 (DCC)
R-Value Work:
0.190 (Depositor)
R-Value Observed:
0.192 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 3H8S

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
Modeled Residue Count: 284
Deposited Residue Count: 305
Unique protein chains: 1

Macromolecules

Find similar proteins by:

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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% 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] mmCIF 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 (Depositor), 0.241 (DCC)
R-Value Work: 0.190 (Depositor)
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

View Full Validation Report

View more in-depth experimental data

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 is hosted by

RCSB PDB is a member of

RCSB Partners
Nucleic Acid Knowledgebase

CoreTrustSeal

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), 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 R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.