Download MendeleyThe structure of a putative DNA-binding protein from Bacteroides fragilis.
Cuff, M.E., Bigelow, L., Clancy, S., Joachimiak, A.To be published.
3BS3 | pdb_00003bs3
Crystal structure of a putative DNA-binding protein from Bacteroides fragilis
- PDB DOI: https://doi.org/10.2210/pdb3BS3/pdb
- Classification: DNA BINDING PROTEIN
- Organism(s): Bacteroides fragilis NCTC 9343
- Expression System: Escherichia coli BL21(DE3)
- Mutation(s): No
- Deposited: 2007-12-21 Released: 2008-01-15
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.65 Å
- R-Value Free: 0.219 (Depositor), 0.216 (DCC)
- R-Value Work: 0.183 (Depositor), 0.182 (DCC)
- R-Value Observed: 0.185 (Depositor)
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 |
| Putative DNA-binding protein | 76 | Bacteroides fragilis NCTC 9343 | Mutation(s): 0 Gene Names: BF1076 |  | |
UniProt | |||||
Find proteins for Q5LGD2 (Bacteroides fragilis (strain ATCC 25285 / DSM 2151 / CCUG 4856 / JCM 11019 / LMG 10263 / NCTC 9343 / Onslow / VPI 2553 / EN-2)) Explore Q5LGD2 Go to UniProtKB: Q5LGD2 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | Q5LGD2 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Small Molecules
| Ligands 2 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| SO4 Query on SO4 | B [auth A] | SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L |  | ||
| EDO Query on EDO | C [auth A] | 1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-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: 1.65 Å
- R-Value Free: 0.219 (Depositor), 0.216 (DCC)
- R-Value Work: 0.183 (Depositor), 0.182 (DCC)
- R-Value Observed: 0.185 (Depositor)
Space Group: P 31 2 1
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 63.337 | α = 90 |
| b = 63.337 | β = 90 |
| c = 34.706 | γ = 120 |
| 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: 2008-01-15 Deposition Author(s): Cuff, M.E., Bigelow, L., Clancy, S., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)
Revision History (Full details and data files)
- Version 1.0: 2008-01-15
Type: Initial release - Version 1.1: 2011-07-13
Changes: Advisory, Source and taxonomy, Version format compliance - Version 1.2: 2017-10-25
Changes: Refinement description - Version 1.3: 2024-10-30
Changes: Data collection, Database references, Derived calculations, Structure summary
