6LS1

Ribonuclease from Hericium erinaceus active and GMP binding form

PDB DOI: https://doi.org/10.2210/pdb6LS1/pdb

Classification: RNA BINDING PROTEIN
Organism(s): Hericium erinaceus
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2020-01-16 Released: 2021-01-20
Deposition Author(s): Takebe, K., Suzuki, M., Sangawa, T., Kobayashi, H., Itagaki, T.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.58 ?
R-Value Free: 0.190
R-Value Work: 0.149
R-Value Observed: 0.151

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

Ribonuclease from Hericium erinaceus active and GMP binding form

Takebe, K., Suzuki, M., Sangawa, T., Kobayashi, H.

To be published.

Macromolecule Content

Total Structure Weight: 21.92 kDa
Atom Count: 1,756
Modelled Residue Count: 200
Deposited Residue Count: 200
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribonuclease T1	A, B	100	Hericium erinaceus	Mutation(s): 0 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 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GMP (Subject of Investigation/LOI) Query on GMP 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]	GUANOSINE C₁₀ H₁₃ N₅ O₅ NYHBQMYGNKIUIF-UUOKFMHZSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
PEG Query on PEG Download Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]
SO4 Query on SO4 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]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain E [auth B] Interactions & Density Focus chain E [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.58 ?
R-Value Free: 0.190
R-Value Work: 0.149
R-Value Observed: 0.151
Space Group: I 4 2 2

Unit Cell:

Length ( ? )	Angle ( ? )
a = 97.76	α = 90
b = 97.76	β = 90
c = 68.91	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2021-01-20

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2021-01-20
Type: Initial release
Version 1.1: 2023-11-29
Changes: Data collection, Database references, Refinement description
Version 1.2: 2024-10-23
Changes: Structure summary

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Deposit Data

Help and Resources

6LS1

Ribonuclease from Hericium erinaceus active and GMP binding form

Ribonuclease from Hericium erinaceus active and GMP binding form

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

Expand

Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)