Download MendeleyStructure of the C-terminal domains of a LysR family protein from Agrobacterium tumefaciens str. C58.
Cuff, M.E., Xu, X., Zeng, H., Edwards, A., Savchenko, A., Joachimiak, A.To be published.
3FD3
Structure of the C-terminal domains of a LysR family protein from Agrobacterium tumefaciens str. C58.
- PDB DOI: https://doi.org/10.2210/pdb3FD3/pdb
- Classification: transcription regulator
- Organism(s): Agrobacterium fabrum str. C58
- Expression System: Escherichia coli
- Mutation(s): No
- Deposited: 2008-11-24 Released: 2009-02-03
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.70 Å
- R-Value Free: 0.200
- R-Value Work: 0.169
- R-Value Observed: 0.171
wwPDB Validation 3D Report Full Report
This is version 1.3 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 |
| chromosome replication initiation inhibitor protein | 208 | Agrobacterium fabrum str. C58 | Mutation(s): 0 Gene Names: AGR_C_1691, Atu0928, oriC |  | |
UniProt | |||||
Find proteins for A9CJQ0 (Agrobacterium fabrum (strain C58 / ATCC 33970)) Explore A9CJQ0 Go to UniProtKB: A9CJQ0 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | A9CJQ0 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Small Molecules
| Ligands 4 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| P33 Query on P33 | C [auth A] | 3,6,9,12,15,18-HEXAOXAICOSANE-1,20-DIOL C14 H30 O8 XPJRQAIZZQMSCM-UHFFFAOYSA-N |  | ||
| PG4 Query on PG4 | D [auth A] | TETRAETHYLENE GLYCOL C8 H18 O5 UWHCKJMYHZGTIT-UHFFFAOYSA-N |  | ||
| EDO Query on EDO | E [auth A] | 1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N |  | ||
| CA Query on CA | B [auth A] | CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N |  | ||
| Modified Residues 1 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Type | Formula | 2D Diagram | Parent |
| MSE Query on MSE | A | L-PEPTIDE LINKING | C5 H11 N O2 Se |  | MET |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 1.70 Å
- R-Value Free: 0.200
- R-Value Work: 0.169
- R-Value Observed: 0.171
- Space Group: P 43 21 2
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 53.613 | α = 90 |
| b = 53.613 | β = 90 |
| c = 188.027 | γ = 90 |
| Software Name | Purpose |
|---|---|
| DENZO | data reduction |
| SCALEPACK | data scaling |
| MLPHARE | phasing |
| DM | phasing |
| REFMAC | refinement |
| PDB_EXTRACT | data extraction |
| SBC-Collect | data collection |
| HKL-3000 | data reduction |
| HKL-3000 | data scaling |
| HKL-3000 | phasing |
| SHELXD | phasing |
| SHELXE | model building |
| SOLVE | phasing |
| RESOLVE | phasing |
| ARP/wARP | model building |
| CCP4 | phasing |
| O | model building |
| Coot | model building |
Entry History
Deposition Data
- Released Date: 2009-02-03 Deposition Author(s): Cuff, M.E., Xu, X., Zeng, H., Edwards, A., Savchenko, A., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)
Revision History (Full details and data files)
- Version 1.0: 2009-02-03
Type: Initial release - Version 1.1: 2011-07-13
Changes: Advisory, Refinement description, Source and taxonomy, Version format compliance - Version 1.2: 2017-11-01
Changes: Refinement description - Version 1.3: 2023-12-27
Changes: Data collection, Database references, Derived calculations, Structure summary
