5GY6 | pdb_00005gy6

Ribonuclease from Hericium erinaceus (RNase He1)

PDB DOI: https://doi.org/10.2210/pdb5GY6/pdb

Classification: HYDROLASE
Organism(s): Hericium erinaceus
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2016-09-21 Released: 2017-09-27
Deposition Author(s): Kobayashi, H., Sangawa, T., Takebe, K., Itagaki, T., Motoyoshi, N., Suzuki, M.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.50 Å
R-Value Free:
0.197 (Depositor), 0.201 (DCC)
R-Value Work:
0.172 (Depositor), 0.174 (DCC)
R-Value Observed:
0.174 (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

Ribonuclease from Hericium erinaceus (RNase He1)

Kobayashi, H., Sangawa, T., Takebe, K., Itagaki, T., Motoyoshi, N., Suzuki, M.

To be published.

Macromolecule Content

Total Structure Weight: 10.78 kDa
Atom Count: 824
Modeled Residue Count: 88
Deposited Residue Count: 100
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribonuclease T1	A	100	Hericium erinaceus	Mutation(s): 0 Gene Names: RNHe1 EC: 3.1.27.3
UniProt
Find proteins for B1Q4V2 (Hericium erinaceus) Explore B1Q4V2 Go to UniProtKB: B1Q4V2
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	B1Q4V2
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ZN Query on ZN 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]	ZINC ION Zn PTFCDOFLOPIGGS-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: 1.50 Å
R-Value Free: 0.197 (Depositor), 0.201 (DCC)
R-Value Work: 0.172 (Depositor), 0.174 (DCC)
R-Value Observed: 0.174 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 31.701	α = 90
b = 42.945	β = 90
c = 60.183	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
SCALA	data scaling
MOLREP	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2017-09-27

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2017-09-27
Type: Initial release
Version 1.1: 2023-11-08
Changes: Data collection, Database references, Refinement description
Version 1.2: 2024-11-13
Changes: Structure summary

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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.