Download MendeleyCrystal structure of SusD homolog (YP_212639.1) from Bacteroides fragilis NCTC 9343 at 1.50 A resolution
Joint Center for Structural Genomics (JCSG)To be published.
3EJN | pdb_00003ejn
3EJN | pdb_00003ejn
CRYSTAL STRUCTURE OF A SUSD HOMOLOG (BF3025) FROM BACTEROIDES FRAGILIS NCTC 9343 AT 1.50 A RESOLUTION
- PDB DOI: https://doi.org/10.2210/pdb3EJN/pdb
- Classification: SUGAR BINDING PROTEIN
- Organism(s): Bacteroides fragilis NCTC 9343
- Expression System: Escherichia coli
- Mutation(s): No
- Deposited: 2008-09-18 Released: 2008-09-30
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.50 Å
- R-Value Free: 0.168 (Depositor), 0.159 (DCC)
- R-Value Work: 0.154 (Depositor), 0.162 (DCC)
- R-Value Observed: 0.155 (Depositor)
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:
| 3D Structure
Entity ID: 1 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| SusD homolog | 474 | Bacteroides fragilis NCTC 9343 | Mutation(s): 0 Gene Names: YP_212639.1, BF3025 |  | |
UniProt | |||||
Find proteins for A0A380YV80 (Bacteroides fragilis (strain ATCC 25285 / DSM 2151 / CCUG 4856 / JCM 11019 / LMG 10263 / NCTC 9343 / Onslow / VPI 2553 / EN-2)) Explore A0A380YV80 Go to UniProtKB: A0A380YV80 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | A0A380YV80 | ||||
Sequence AnnotationsExpand | |||||
Reference Sequence | |||||
Small Molecules
| Ligands 3 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| PG4 Download:Ideal Coordinates CCD File | B [auth A], C [auth A], D [auth A] | TETRAETHYLENE GLYCOL C8 H18 O5 UWHCKJMYHZGTIT-UHFFFAOYSA-N |  | ||
| FMT Download:Ideal Coordinates CCD File | E [auth A], F [auth A], G [auth A], H [auth A] | FORMIC ACID C H2 O2 BDAGIHXWWSANSR-UHFFFAOYSA-N |  | ||
| MG Download:Ideal Coordinates CCD File | I [auth A] | MAGNESIUM ION Mg JLVVSXFLKOJNIY-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: 1.50 Å
- R-Value Free: 0.168 (Depositor), 0.159 (DCC)
- R-Value Work: 0.154 (Depositor), 0.162 (DCC)
- R-Value Observed: 0.155 (Depositor)
Diffraction Data:
Space Group: H 3
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 166.99 | α = 90 |
| b = 166.99 | β = 90 |
| c = 48.94 | γ = 120 |
| Software Name | Purpose |
|---|---|
| REFMAC | refinement |
| PHENIX | refinement |
| SHELX | phasing |
| MolProbity | model building |
| XSCALE | data scaling |
| PDB_EXTRACT | data extraction |
| XDS | data reduction |
| SHELXD | phasing |
| autoSHARP | phasing |
Entry History
Deposition Data
- Released Date: 2008-09-30 Deposition Author(s): Joint Center for Structural Genomics (JCSG)
Revision History (Full details and data files)
- Version 1.0: 2008-09-30
Type: Initial release - Version 1.1: 2011-07-13
Changes: Version format compliance - Version 1.2: 2017-10-25
Changes: Refinement description - Version 1.3: 2019-07-24
Changes: Data collection, Derived calculations, Refinement description - Version 1.4: 2023-02-01
Changes: Database references, Derived calculations - Version 1.5: 2024-11-13
Changes: Data collection, Structure summary
