2EA1 | pdb_00002ea1

Crystal structure of Ribonuclease I from Escherichia coli COMPLEXED WITH GUANYLYL-2(PRIME),5(PRIME)-GUANOSINE

PDB DOI: https://doi.org/10.2210/pdb2EA1/pdb

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

Deposited: 2007-01-29 Released: 2008-01-22
Deposition Author(s): Zhou, K., Pan, J., Padmanabhan, S., Lim, R.W., Lim, L.W.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free:
0.257 (Depositor), 0.258 (DCC)
R-Value Work:
0.218 (Depositor), 0.217 (DCC)
R-Value Observed:
0.220 (Depositor)

wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment

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

Literature

Crystal Structure of Ribonuclease I from Escherichia Coli Complexed with Guanylyl-2(Prime),5(Prime)-Guanosine at 1.80 Angstroms Resolution

Zhou, K., Pan, J., Padmanabhan, S., Lim, R.W., Lim, L.W.

To be published.

Macromolecule Content

Total Structure Weight: 27.82 kDa
Atom Count: 2,094
Modeled Residue Count: 245
Deposited Residue Count: 245
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribonuclease I	A	245	Escherichia coli	Mutation(s): 0 EC: 3.1.27.6 (PDB Primary Data), 4.6.1.21 (UniProt)
UniProt
Find proteins for P21338 (Escherichia coli (strain K12)) Explore P21338 Go to UniProtKB: P21338
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P21338
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GPG Query on GPG 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]	GUANYLYL-2',5'-PHOSPHOGUANOSINE C₂₀ H₂₅ N₁₀ O₁₂ P YYNDAHWXMRBBRC-MHARETSRSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free: 0.257 (Depositor), 0.258 (DCC)
R-Value Work: 0.218 (Depositor), 0.217 (DCC)
R-Value Observed: 0.220 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 43.2	α = 90
b = 49.87	β = 96.37
c = 54.52	γ = 90

Software Package:

Software Name	Purpose
AMoRE	phasing
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2008-01-22

Deposition Author(s):

Padmanabhan, S.

Revision History (Full details and data files)

Version 1.0: 2008-01-22
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2024-10-16
Changes: Data collection, Database references, Derived calculations, 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.