7N8W | pdb_00007n8w

Crystal structure of ERI2 nuclease bound to rAMP

PDB DOI: https://doi.org/10.2210/pdb7N8W/pdb

Classification: HYDROLASE
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2021-06-15 Released: 2022-07-06
Deposition Author(s): Thapar, R., Arvai, A.S., Tainer, J.A.
Funding Organization(s): Robert A. Welch Foundation, National Institutes of Health/National Cancer Institute (NIH/NCI), Other private, National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.35 Å
R-Value Free:
0.223 (Depositor), 0.220 (DCC)
R-Value Work:
0.179 (Depositor), 0.180 (DCC)
R-Value Observed:
0.181 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Crystal structure of ERI2 nuclease bound to rAMP

Thapar, R., Arvai, A.S., Tainer, J.A.

To be published.

Macromolecule Content

Total Structure Weight: 60.75 kDa
Atom Count: 3,484
Modeled Residue Count: 427
Deposited Residue Count: 528
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ERI1 exoribonuclease 2	A, B	264	Homo sapiens	Mutation(s): 0 Gene Names: ERI2, EXOD1, KIAA1504 EC: 3.1
UniProt & NIH Common Fund Data Resources
Find proteins for A8K979 (Homo sapiens) Explore A8K979 Go to UniProtKB: A8K979
PHAROS: A8K979 GTEx: ENSG00000196678
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A8K979
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
AMP (Subject of Investigation/LOI) Query on AMP Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	ADENOSINE MONOPHOSPHATE C₁₀ H₁₄ N₅ O₇ P UDMBCSSLTHHNCD-KQYNXXCUSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain H [auth B] SDF format, chain G [auth B] SDF format, chain F [auth B] SDF format, chain D [auth A] MOL2 format, chain H [auth B] MOL2 format, chain G [auth B] MOL2 format, chain F [auth B] MOL2 format, chain D [auth A] mmCIF format, chain H [auth B] mmCIF format, chain G [auth B] mmCIF format, chain F [auth B] mmCIF format, chain D [auth A]	D [auth A], F [auth B], G [auth B], H [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain D [auth A] Focus chain F [auth B] Focus chain G [auth B] Focus chain H [auth B] Interactions & Density Focus chain D [auth A] Focus chain F [auth B] Focus chain G [auth B] Focus chain H [auth B]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain I [auth B] MOL2 format, chain I [auth B] mmCIF format, chain I [auth B]	I [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain I [auth B] Interactions & Density Focus chain I [auth B]
MN (Subject of Investigation/LOI) Query on MN Download Ideal Coordinates CCD File SDF format, chain E [auth B] MOL2 format, chain E [auth B] mmCIF format, chain E [auth B]	E [auth B]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N		Interactions Focus chain E [auth B] Interactions & Density Focus chain E [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.35 Å
R-Value Free: 0.223 (Depositor), 0.220 (DCC)
R-Value Work: 0.179 (Depositor), 0.180 (DCC)
R-Value Observed: 0.181 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 60.832	α = 90
b = 56.338	β = 104.572
c = 75.852	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2022-07-06

Deposition Author(s):

Thapar, R.

Arvai, A.S.

Tainer, J.A.

Funding Organization	Location	Grant Number
Robert A. Welch Foundation		--
National Institutes of Health/National Cancer Institute (NIH/NCI)	United States	CA220430
Other private	United States	GAP Award (to R.T., J.A.T)
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R01 GM076660-04S1
National Institutes of Health/National Cancer Institute (NIH/NCI)	United States	P01 CA092584