5CHI | pdb_00005chi

Crystal structure of PF2046 in complex with ssDNA

PDB DOI: https://doi.org/10.2210/pdb5CHI/pdb
NAKB: 5CHI

Classification: HYDROLASE/DNA
Organism(s): Pyrococcus furiosus DSM 3638, synthetic construct
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2015-07-10 Released: 2016-08-10
Deposition Author(s): Kim, J.S., Hwang, K.Y., Lee, W.C.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.47 Å
R-Value Free:
0.228 (Depositor), 0.232 (DCC)
R-Value Work:
0.182 (Depositor), 0.186 (DCC)
R-Value Observed:
0.186 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.2 of the entry. See complete history.

Literature

Structural basis of two-nucleotide removal of ssDNA by a cryptic RNase H fold 3'-5' exonuclease PF2046 from Pyrococcus furiosus

Kim, J.S., Sambalkhundev, G.D., Kim, S.H., Han, A., Ko, S.M., Hwang, K.Y., Lee, W.C.

To be published.

Macromolecule Content

Total Structure Weight: 80.9 kDa
Atom Count: 5,755
Modeled Residue Count: 699
Deposited Residue Count: 702
Unique protein chains: 1
Unique nucleic acid chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Uncharacterized protein	A, B, C	230	Pyrococcus furiosus DSM 3638	Mutation(s): 0 Gene Names: PF2046
UniProt
Find proteins for Q8TZE9 (Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1)) Explore Q8TZE9 Go to UniProtKB: Q8TZE9
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8TZE9
Sequence Annotations Expand
Reference Sequence

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Molecule	Chains	Length	Organism	Image
Entity ID: 2
DNA (5'-D(PTPTPTPT)-3')	D, E, F	4	synthetic construct
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 J [auth B] SDF format, chain I [auth B] SDF format, chain H [auth A] SDF format, chain G [auth A] MOL2 format, chain J [auth B] MOL2 format, chain I [auth B] MOL2 format, chain H [auth A] MOL2 format, chain G [auth A] mmCIF format, chain J [auth B] mmCIF format, chain I [auth B] mmCIF format, chain H [auth A] mmCIF format, chain G [auth A]	G [auth A], H [auth A], I [auth B], J [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth B] Focus chain J [auth B] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth B] Focus chain J [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.47 Å
R-Value Free: 0.228 (Depositor), 0.232 (DCC)
R-Value Work: 0.182 (Depositor), 0.186 (DCC)
R-Value Observed: 0.186 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 69.01	α = 90
b = 85.903	β = 118.44
c = 69.204	γ = 90

Software Package:

Software Name	Purpose
XSCALE	data scaling
MOLREP	model building
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data reduction

Structure Validation

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Entry History

Deposition Data

Released Date: 2016-08-10

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2016-08-10
Type: Initial release
Version 1.1: 2017-09-27
Changes: Data collection, Derived calculations
Version 1.2: 2023-11-08
Changes: Data collection, Database references, Derived calculations, 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.