Download MendeleyStabilizing DNA-Protein Co-Crystals via Intra-Crystal Chemical Ligation of the DNA
Ward, A.R., Dmytriw, S., Vajapayajula, A., Snow, C.D.(2022) Crystals (Basel) 12
7SGC
Replication Initiator Protein REPE54 and cognate DNA sequence with terminal five prime phosphates.
- PDB DOI: https://doi.org/10.2210/pdb7SGC/pdb
- NAKB: 7SGC
- Classification: DNA BINDING PROTEIN/DNA
- Organism(s): Escherichia coli
- Expression System: Escherichia coli
- Mutation(s): Yes
- Deposited: 2021-10-05 Released: 2021-10-13
- Funding Organization(s): National Science Foundation (NSF, United States)
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.70 Å
- R-Value Free: 0.245
- R-Value Work: 0.186
- R-Value Observed: 0.189
Starting Model: experimental
View more details
wwPDB Validation 3D Report Full Report
This is version 1.2 of the entry. See complete history.
Literature
Macromolecules
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 3 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| RepB family plasmid replication initiator protein | 263 | Escherichia coli | Mutation(s): 1 Gene Names: repE, RepE, repE_1, repE_2, A9P13_27925, ACN81_13795, AKG29_00005, AM270_25025, AM446_00510, AM465_27515... |  | |
UniProt | |||||
Find proteins for P03856 (Escherichia coli (strain K12)) Explore P03856 Go to UniProtKB: P03856 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | P03856 | ||||
Sequence AnnotationsExpand | |||||
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Find similar proteins by: Sequence | 3D Structure
Entity ID: 4 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Unidentified polymer | D [auth G] | 3 | Escherichia coli | Mutation(s): 0 |  |
Sequence AnnotationsExpand | |||||
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Find similar proteins by: Sequence | 3D Structure
Entity ID: 5 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Unidentified polymer | E [auth D] | 4 | Escherichia coli | Mutation(s): 0 |  |
Sequence AnnotationsExpand | |||||
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Find similar nucleic acids by: Sequence | 3D Structure
Entity ID: 1 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Length | Organism | Image | |
| DNA (5'-D(P*CP*CP*TP*GP*TP*GP*AP*CP*AP*AP*AP*TP*TP*GP*CP*CP*CP*TP*CP*AP*G)-3') | 21 | Escherichia coli |  | ||
Sequence AnnotationsExpand | |||||
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Find similar nucleic acids by: Sequence | 3D Structure
Entity ID: 2 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Length | Organism | Image | |
| DNA (5'-D(P*CP*TP*GP*AP*GP*GP*GP*CP*AP*AP*TP*TP*TP*GP*TP*CP*AP*CP*AP*GP*G)-3') | 21 | Escherichia coli |  | ||
Sequence AnnotationsExpand | |||||
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Small Molecules
| Ligands 1 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| MG Query on MG | F [auth C], G [auth C], H [auth C] | MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N |  | ||
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.70 Å
- R-Value Free: 0.245
- R-Value Work: 0.186
- R-Value Observed: 0.189
- Space Group: C 1 2 1
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 109.161 | α = 90 |
| b = 83.051 | β = 123.948 |
| c = 74.349 | γ = 90 |
| Software Name | Purpose |
|---|---|
| PHENIX | refinement |
| Coot | model building |
| XDS | data reduction |
| XSCALE | data scaling |
| SCALA | data scaling |
| PHASER | phasing |
Entry History & Funding Information
Deposition Data
- Released Date: 2021-10-13 Deposition Author(s): Ward, A.R., Snow, C.D.
| Funding Organization | Location | Grant Number |
|---|---|---|
| National Science Foundation (NSF, United States) | United States | 2003748 |
Revision History (Full details and data files)
- Version 1.0: 2021-10-13
Type: Initial release - Version 1.1: 2022-12-14
Changes: Database references - Version 1.2: 2023-10-25
Changes: Data collection, Refinement description
