1BXI | pdb_00001bxi

CRYSTAL STRUCTURE OF THE ESCHERICHIA COLI COLICIN E9 DNASE DOMAIN WITH ITS COGNATE IMMUNITY PROTEIN IM9

PDB DOI: https://doi.org/10.2210/pdb1BXI/pdb

Classification: IMMUNE SYSTEM
Organism(s): Escherichia coli
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 1998-10-04 Released: 1999-10-04
Deposition Author(s): Kuhlmann, U.C., Kleanthous, C., James, R., Moore, G.R., Hemmings, A.M.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.05 Å
R-Value Free:
0.315 (Depositor), 0.287 (DCC)
R-Value Work:
0.218 (Depositor), 0.205 (DCC)

wwPDB Validation 3D Report Full Report

Validation slider image for 1BXI

This is version 1.6 of the entry. See complete history.

Literature

Crystal Structure of the E.Coli Colicin E9 DNase Domain With its Cognate Immunity Protein Im9

(1998) Thesis

Macromolecule Content

Total Structure Weight: 24.89 kDa
Atom Count: 1,794
Modeled Residue Count: 214
Deposited Residue Count: 220
Unique protein chains: 2

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PROTEIN (COLICIN E9 IMMUNITY PROTEIN)	A	86	Escherichia coli	Mutation(s): 1 Gene Names: E9IMM
UniProt
Find proteins for P13479 (Escherichia coli) Explore P13479 Go to UniProtKB: P13479
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P13479
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
PROTEIN (COLICIN E9)	B	134	Escherichia coli	Mutation(s): 2 Gene Names: COLE9 EC: 3.1
UniProt
Find proteins for P09883 (Escherichia coli) Explore P09883 Go to UniProtKB: P09883
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P09883
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PO4 Query on PO4 Download:Ideal Coordinates CCD File SDF format, chain D [auth B] MOL2 format, chain D [auth B] mmCIF format, chain D [auth B]	D [auth B]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain D [auth B] Interactions & Density Focus chain D [auth B]
NI Query on NI Download:Ideal Coordinates CCD File SDF format, chain C [auth B] MOL2 format, chain C [auth B] mmCIF format, chain C [auth B]	C [auth B]	NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N		Interactions Focus chain C [auth B] Interactions & Density Focus chain C [auth B]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	B	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.05 Å
R-Value Free: 0.315 (Depositor), 0.287 (DCC)
R-Value Work: 0.218 (Depositor), 0.205 (DCC)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 43.85	α = 90
b = 51.96	β = 90
c = 87.59	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

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Entry History

Deposition Data

Released Date: 1999-10-04

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 1999-10-04
Type: Initial release
Version 1.1: 2008-04-27
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2018-03-14
Changes: Data collection, Database references
Version 1.4: 2021-11-03
Changes: Database references, Derived calculations
Version 1.5: 2023-12-27
Changes: Data collection
Version 1.6: 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.