3GKL | pdb_00003gkl

Following evolutionary paths to high affinity and selectivity protein-protein interactions using Colicin7 and Immunity proteins

PDB DOI: https://doi.org/10.2210/pdb3GKL/pdb

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

Deposited: 2009-03-11 Released: 2009-09-08
Deposition Author(s): Dym, O., Tawfik, D.S., Israel Structural Proteomics Center (ISPC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free:
0.277 (Depositor), 0.314 (DCC)
R-Value Work:
0.240 (Depositor), 0.268 (DCC)
R-Value Observed:
0.241 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.3 of the entry. See complete history.

Literature

Following evolutionary paths to high affinity and selectivity protein-protein interactions

Bernath, K., Dym, O., Albeck, S., Magdassi, S., Keeble, A., Kleanthous, C., Tawfik, D.S.

To be published.

Macromolecule Content

Total Structure Weight: 51.6 kDa
Atom Count: 3,223
Modeled Residue Count: 404
Deposited Residue Count: 454
Unique protein chains: 2

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Colicin-E9 immunity protein	A, B	141	Escherichia coli	Mutation(s): 9 Gene Names: colE7, cea EC: 3.1
UniProt
Find proteins for Q47112 (Escherichia coli) Explore Q47112 Go to UniProtKB: Q47112
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q47112
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Colicin-E7	C, D	86	Escherichia coli	Mutation(s): 9 Gene Names: imm, ceiE9
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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain F [auth B] SDF format, chain E [auth A] MOL2 format, chain F [auth B] MOL2 format, chain E [auth A] mmCIF format, chain F [auth B] mmCIF format, chain E [auth A]	E [auth A], F [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth B] Interactions & Density Focus chain E [auth A] Focus chain F [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.277 (Depositor), 0.314 (DCC)
R-Value Work: 0.240 (Depositor), 0.268 (DCC)
R-Value Observed: 0.241 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 54.161	α = 90
b = 67.371	β = 90
c = 123.231	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
PHASER	phasing
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	data scaling

Structure Validation

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Entry History

Deposition Data

Released Date: 2009-09-08

Deposition Author(s):

Israel Structural Proteomics Center (ISPC)

Revision History (Full details and data files)

Version 1.0: 2009-09-08
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2021-10-20
Changes: Database references, Derived calculations
Version 1.3: 2023-09-06
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.