6SSO | pdb_00006sso

EDN mutant L45H

PDB DOI: https://doi.org/10.2210/pdb6SSO/pdb

Classification: HYDROLASE
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2019-09-08 Released: 2021-10-06
Deposition Author(s): Fernandez-Millan, P., Prats-Ejarque, G., Vazquez-Monteagudo, S., Boix, E.
Funding Organization(s): Spanish Ministry of Economy and Competitiveness

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.21 Å
R-Value Free:
0.151 (Depositor), 0.150 (DCC)
R-Value Work:
0.135 (Depositor), 0.130 (DCC)
R-Value Observed:
0.136 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

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

Literature

Structural and functional characterization of new family enzymes derivates from human RNase 1 and 3 with antimicrobial and ribonuclease activity

Fernandez-Millan, P., Prats-Ejarque, G., Vazquez-Monteagudo, S., Boix, E.

To be published.

Macromolecule Content

Total Structure Weight: 15.7 kDa
Atom Count: 1,410
Modeled Residue Count: 135
Deposited Residue Count: 135
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Non-secretory ribonuclease	A	135	Homo sapiens	Mutation(s): 1 Gene Names: RNASE2, EDN, RNS2 EC: 4.6.1.18
UniProt & NIH Common Fund Data Resources
Find proteins for P10153 (Homo sapiens) Explore P10153 Go to UniProtKB: P10153
PHAROS: P10153 GTEx: ENSG00000169385
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P10153
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ACT Query on ACT 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]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.21 Å
R-Value Free: 0.151 (Depositor), 0.150 (DCC)
R-Value Work: 0.135 (Depositor), 0.130 (DCC)
R-Value Observed: 0.136 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.12	α = 90
b = 52.47	β = 90
c = 56.63	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2021-10-06

Deposition Author(s):

Fernandez-Millan, P.

Prats-Ejarque, G.

Vazquez-Monteagudo, S.

Funding Organization	Location	Grant Number
Spanish Ministry of Economy and Competitiveness	Spain	SAF2015-66007-P

Revision History (Full details and data files)

Version 1.0: 2021-10-06
Type: Initial release
Version 1.1: 2024-01-24
Changes: Data collection, Refinement description
Version 1.2: 2024-11-13
Changes: Structure summary

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.