7W05 | pdb_00007w05

12 mutant Ribonuclease from Hericium erinaceus GMP binding form

PDB DOI: https://doi.org/10.2210/pdb7W05/pdb

Classification: DNA BINDING PROTEIN
Organism(s): Hericium erinaceus
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2021-11-17 Released: 2022-11-23
Deposition Author(s): Takebe, K., Chida, T., Suzuki, M., Itagaki, T., Morita, Y., Uzawa, N., Kobayashi, H.
Funding Organization(s): Japan Society for the Promotion of Science (JSPS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.29 Å
R-Value Free:
0.166 (Depositor), 0.170 (DCC)
R-Value Work:
0.137 (Depositor), 0.140 (DCC)
R-Value Observed:
0.138 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

12 mutant Ribonuclease from Hericium erinaceus GMP binding form

Takebe, K., Chida, T., Suzuki, M., Uzawa, N., Kobayashi, H.

To be published.

Macromolecule Content

Total Structure Weight: 11.09 kDa
Atom Count: 930
Modeled Residue Count: 100
Deposited Residue Count: 100
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribonuclease T1	A	100	Hericium erinaceus	Mutation(s): 12 Gene Names: RNHe1
UniProt
Find proteins for B1Q4V2 (Hericium erinaceus) Explore B1Q4V2 Go to UniProtKB: B1Q4V2
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	B1Q4V2
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GMP Query on GMP 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]	GUANOSINE C₁₀ H₁₃ N₅ O₅ NYHBQMYGNKIUIF-UUOKFMHZSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
PEG (Subject of Investigation/LOI) Query on PEG 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]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.29 Å
R-Value Free: 0.166 (Depositor), 0.170 (DCC)
R-Value Work: 0.137 (Depositor), 0.140 (DCC)
R-Value Observed: 0.138 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 34.589	α = 90
b = 46.31	β = 90
c = 53.524	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
Aimless	data scaling
MOLREP	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2022-11-23

Deposition Author(s):

Funding Organization	Location	Grant Number
Japan Society for the Promotion of Science (JSPS)	Japan	20K21676

Revision History (Full details and data files)

Version 1.0: 2022-11-23
Type: Initial release
Version 1.1: 2023-11-29
Changes: Data collection, Refinement description
Version 1.2: 2024-11-06
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.