Download MendeleyCrystal 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.
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
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.60 Å
- R-Value Free: 0.232 (Depositor), 0.240 (DCC)
- R-Value Work: 0.185 (Depositor), 0.200 (DCC)
- R-Value Observed: 0.187 (Depositor)
Starting Model: experimental
View more details
wwPDB Validation 3D Report Full Report
This is version 1.5 of the entry. See complete history.
Literature
To be published.
Macromolecules
Find similar proteins by:
(by identity cutoff) | 3D Structure
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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | P13479 | ||||
Sequence AnnotationsExpand | |||||
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Find similar proteins by:
(by identity cutoff) | 3D Structure
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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | P09883 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Small Molecules
| Ligands 2 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| PO4 Query on PO4 | F [auth B], H [auth F] | PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K |  | ||
| ZN Query on ZN | E [auth B], G [auth F] | ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N |  | ||
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 1.60 Å
- R-Value Free: 0.232 (Depositor), 0.240 (DCC)
- R-Value Work: 0.185 (Depositor), 0.200 (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 Name | Purpose |
|---|---|
| DENZO | data reduction |
| SCALEPACK | data scaling |
| REFMAC | refinement |
| PDB_EXTRACT | data extraction |
| ADSC | data collection |
| MOLREP | phasing |
Entry History
Deposition Data
- Released Date: 2007-05-15 Deposition Author(s): Santi, P.S., Kolade, O.O., Kuhlmann, U.C., Hemmings, A.M.
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
