2GYK | pdb_00002gyk

Crystal structure of the complex of the Colicin E9 DNase domain with a mutant immunity protein, IMME9 (D51A)

PDB DOI: https://doi.org/10.2210/pdb2GYK/pdb

Classification: antibiotic/antibiotic inhibitor
Organism(s): Escherichia coli K-12
Expression System: Escherichia coli BL21(DE3), Escherichia coli
Mutation(s): Yes

Deposited: 2006-05-09 Released: 2007-05-15
Deposition Author(s): Santi, P.S., Kolade, O.O., Kuhlmann, U.C., Hemmings, A.M.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free:
0.232 (Depositor), 0.242 (DCC)
R-Value Work:
0.185 (Depositor), 0.199 (DCC)
R-Value Observed:
0.187 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.5 of the entry. See complete history.

Literature

Crystal structures of the complexes of the Colicin E9 DNase domain with mutant immunity proteins

Kuhlmann, U.C., Santi, P.S., Kolade, O.O., Moore, G.R., James, R., Kleanthous, C., Hemmings, A.M.

To be published.

Macromolecule Content

Total Structure Weight: 49.66 kDa
Atom Count: 4,109
Modeled Residue Count: 428
Deposited Residue Count: 440
Unique protein chains: 2

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Colicin-E9 immunity protein	A, C [auth E]	86	Escherichia coli K-12	Mutation(s): 1 Gene Names: IMM9_ECOLI
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
Colicin-E9	B, D [auth F]	134	Escherichia coli K-12	Mutation(s): 0 Gene Names: col, cei EC: 3.1.21.1 (PDB Primary Data), 3.1 (UniProt)
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 F [auth B] SDF format, chain H [auth F] MOL2 format, chain F [auth B] MOL2 format, chain H [auth F] mmCIF format, chain F [auth B] mmCIF format, chain H [auth F]	F [auth B], H [auth F]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain F [auth B] Focus chain H [auth F] Interactions & Density Focus chain F [auth B] Focus chain H [auth F]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain E [auth B] SDF format, chain G [auth F] MOL2 format, chain E [auth B] MOL2 format, chain G [auth F] mmCIF format, chain E [auth B] mmCIF format, chain G [auth F]	E [auth B], G [auth F]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain E [auth B] Focus chain G [auth F] Interactions & Density Focus chain E [auth B] Focus chain G [auth F]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free: 0.232 (Depositor), 0.242 (DCC)
R-Value Work: 0.185 (Depositor), 0.199 (DCC)
R-Value Observed: 0.187 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 44.903	α = 90
b = 88.248	β = 91.92
c = 52.235	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
ADSC	data collection
MOLREP	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2007-05-15

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2007-05-15
Type: Initial release
Version 1.1: 2008-05-01
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2017-10-18
Changes: Data collection, Refinement description
Version 1.4: 2021-10-20
Changes: Database references, Derived calculations
Version 1.5: 2023-08-30
Changes: Data collection, Refinement description

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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.