Download MendeleyCrystal structure of Putative sugar binding protein (YP_001300177.1) from Bacteroides vulgatus ATCC 8482 at 1.70 A resolution
Joint Center for Structural Genomics (JCSG)To be published.
3KDW
Crystal structure of Putative sugar binding protein (YP_001300177.1) from Bacteroides vulgatus ATCC 8482 at 1.70 A resolution
- PDB DOI: https://doi.org/10.2210/pdb3KDW/pdb
- Classification: SUGAR BINDING PROTEIN
- Organism(s): Phocaeicola vulgatus ATCC 8482
- Expression System: Escherichia coli
- Mutation(s): No
- Deposited: 2009-10-23 Released: 2009-11-24
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.70 Å
- R-Value Free: 0.191
- R-Value Work: 0.152
- R-Value Observed: 0.154
wwPDB Validation 3D Report Full Report
This is version 1.4 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 sugar binding protein | 221 | Phocaeicola vulgatus ATCC 8482 | Mutation(s): 0 Gene Names: BVU_2916 |  | |
UniProt | |||||
Find proteins for A6L4E1 (Phocaeicola vulgatus (strain ATCC 8482 / DSM 1447 / JCM 5826 / CCUG 4940 / NBRC 14291 / NCTC 11154)) Explore A6L4E1 Go to UniProtKB: A6L4E1 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | A6L4E1 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Small Molecules
| Ligands 4 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| MPD Query on MPD | C [auth A], E [auth A] | (4S)-2-METHYL-2,4-PENTANEDIOL C6 H14 O2 SVTBMSDMJJWYQN-YFKPBYRVSA-N |  | ||
| MRD Query on MRD | D [auth A] | (4R)-2-METHYLPENTANE-2,4-DIOL C6 H14 O2 SVTBMSDMJJWYQN-RXMQYKEDSA-N |  | ||
| PO4 Query on PO4 | F [auth A] G [auth A] H [auth A] I [auth A] J [auth A] | PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K |  | ||
| CL Query on CL | B [auth A] | CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M |  | ||
| 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: 0.191
- R-Value Work: 0.152
- R-Value Observed: 0.154
- Space Group: P 31 2 1
- Diffraction Data: https://doi.org/10.18430/M33KDW
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 75.303 | α = 90 |
| b = 75.303 | β = 90 |
| c = 87.128 | γ = 120 |
| Software Name | Purpose |
|---|---|
| REFMAC | refinement |
| PHENIX | refinement |
| SOLVE | phasing |
| MolProbity | model building |
| XSCALE | data scaling |
| PDB_EXTRACT | data extraction |
| XDS | data reduction |
Entry History
Deposition Data
- Released Date: 2009-11-24 Deposition Author(s): Joint Center for Structural Genomics (JCSG)
Revision History (Full details and data files)
- Version 1.0: 2009-11-24
Type: Initial release - Version 1.1: 2011-07-13
Changes: Advisory, Version format compliance - Version 1.2: 2017-10-25
Changes: Author supporting evidence, Refinement description - Version 1.3: 2019-07-17
Changes: Data collection, Derived calculations, Refinement description - Version 1.4: 2023-02-01
Changes: Database references, Derived calculations
