2IGI | pdb_00002igi

Crystal Structure of E. coli Oligoribonuclease

PDB DOI: https://doi.org/10.2210/pdb2IGI/pdb

Classification: HYDROLASE
Organism(s): Escherichia coli K-12
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2006-09-22 Released: 2007-10-02
Deposition Author(s): Zuo, Y., Malhotra, A.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free:
0.200 (Depositor), 0.190 (DCC)
R-Value Work:
0.177 (Depositor), 0.170 (DCC)
R-Value Observed:
0.177 (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

Crystal Structure of Oligoribonuclease, the lone essential exoribonuclease in Escherichia coli

Fiedler, T.J., Zuo, Y., Malhotra, A.

To be published.

Macromolecule Content

Total Structure Weight: 43.62 kDa
Atom Count: 3,384
Modeled Residue Count: 359
Deposited Residue Count: 360
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Oligoribonuclease	A, B	180	Escherichia coli K-12	Mutation(s): 0 Gene Names: orn EC: 3.1 (PDB Primary Data), 3.1.15 (UniProt)
UniProt
Find proteins for P0A784 (Escherichia coli (strain K12)) Explore P0A784 Go to UniProtKB: P0A784
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P0A784
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CD Query on CD Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain R [auth B] SDF format, chain S [auth B] SDF format, chain U [auth B] SDF format, chain V [auth B] SDF format, chain W [auth B] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain R [auth B] MOL2 format, chain S [auth B] MOL2 format, chain U [auth B] MOL2 format, chain V [auth B] MOL2 format, chain W [auth B] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A] mmCIF format, chain L [auth A] mmCIF format, chain R [auth B] mmCIF format, chain S [auth B] mmCIF format, chain U [auth B] mmCIF format, chain V [auth B] mmCIF format, chain W [auth B]	D [auth A] E [auth A] G [auth A] H [auth A] I [auth A] D [auth A], E [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], L [auth A], R [auth B], S [auth B], U [auth B], V [auth B], W [auth B]	CADMIUM ION Cd WLZRMCYVCSSEQC-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain R [auth B] Focus chain S [auth B] Focus chain U [auth B] Focus chain V [auth B] Focus chain W [auth B] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain R [auth B] Focus chain S [auth B] Focus chain U [auth B] Focus chain V [auth B] Focus chain W [auth B]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain F [auth A] SDF format, chain Q [auth B] SDF format, chain T [auth B] MOL2 format, chain C [auth A] MOL2 format, chain F [auth A] MOL2 format, chain Q [auth B] MOL2 format, chain T [auth B] mmCIF format, chain C [auth A] mmCIF format, chain F [auth A] mmCIF format, chain Q [auth B] mmCIF format, chain T [auth B]	C [auth A], F [auth A], Q [auth B], T [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain F [auth A] Focus chain Q [auth B] Focus chain T [auth B] Interactions & Density Focus chain C [auth A] Focus chain F [auth A] Focus chain Q [auth B] Focus chain T [auth B]
ACY Query on ACY Download Ideal Coordinates CCD File SDF format, chain AA [auth B] SDF format, chain M [auth A] SDF format, chain N [auth A] SDF format, chain O [auth A] SDF format, chain P [auth A] SDF format, chain X [auth B] SDF format, chain Y [auth B] SDF format, chain Z [auth B] MOL2 format, chain AA [auth B] MOL2 format, chain M [auth A] MOL2 format, chain N [auth A] MOL2 format, chain O [auth A] MOL2 format, chain P [auth A] MOL2 format, chain X [auth B] MOL2 format, chain Y [auth B] MOL2 format, chain Z [auth B] mmCIF format, chain AA [auth B] mmCIF format, chain M [auth A] mmCIF format, chain N [auth A] mmCIF format, chain O [auth A] mmCIF format, chain P [auth A] mmCIF format, chain X [auth B] mmCIF format, chain Y [auth B] mmCIF format, chain Z [auth B]	AA [auth B] M [auth A] N [auth A] O [auth A] P [auth A] AA [auth B], M [auth A], N [auth A], O [auth A], P [auth A], X [auth B], Y [auth B], Z [auth B]	ACETIC ACID C₂ H₄ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-N		Interactions Focus chain AA [auth B] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain X [auth B] Focus chain Y [auth B] Focus chain Z [auth B] Interactions & Density Focus chain AA [auth B] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain X [auth B] Focus chain Y [auth B] Focus chain Z [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free: 0.200 (Depositor), 0.190 (DCC)
R-Value Work: 0.177 (Depositor), 0.170 (DCC)
R-Value Observed: 0.177 (Depositor)

Space Group: P 6₅

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 91.55	α = 90
b = 91.55	β = 90
c = 111.18	γ = 120

Software Package:

Software Name	Purpose
CNS	refinement
CBASS	data collection
DENZO	data reduction
SCALEPACK	data scaling
CNS	phasing

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2007-10-02

Deposition Author(s):

Zuo, Y.

Malhotra, A.

Revision History (Full details and data files)

Version 1.0: 2007-10-02
Type: Initial release
Version 1.1: 2011-07-13
Changes: Derived calculations, Source and taxonomy, Version format compliance
Version 1.2: 2023-08-30
Changes: Data collection, Database references, Derived calculations, Refinement description