3H7I | pdb_00003h7i

Structure of the metal-free D132N T4 RNase H

PDB DOI: https://doi.org/10.2210/pdb3H7I/pdb

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

Deposited: 2009-04-27 Released: 2010-05-12
Deposition Author(s): Tomanicek, S.J., Mueser, T.C.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.50 Å
R-Value Free:
0.213 (Depositor), 0.205 (DCC)
R-Value Work:
0.180 (Depositor), 0.175 (DCC)
R-Value Observed:
0.181 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 3H7I

This is version 1.3 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: 35.8 kDa
Atom Count: 2,832
Modeled Residue Count: 302
Deposited Residue Count: 305
Unique protein chains: 1

Macromolecules

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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
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain B [auth A] MOL2 format, chain C [auth A] MOL2 format, chain B [auth A] mmCIF format, chain C [auth A] mmCIF format, chain B [auth A]	B [auth A], C [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain B [auth A] Focus chain C [auth A] Interactions & Density Focus chain B [auth A] Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.50 Å
R-Value Free: 0.213 (Depositor), 0.205 (DCC)
R-Value Work: 0.180 (Depositor), 0.175 (DCC)
R-Value Observed: 0.181 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 36.011	α = 90
b = 85.858	β = 92
c = 57.26	γ = 90

Software Package:

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

Structure Validation

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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: 2021-10-13
Changes: Database references, Derived calculations
Version 1.3: 2023-09-06
Changes: Data collection, Refinement description

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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.