Download MendeleyCrystal structure of hypothetical protein (YP_555756.1) from Burkholderia xenovorans LB400 at 1.55 A resolution
Joint Center for Structural Genomics (JCSG)To be published.
2O8Q
CRYSTAL STRUCTURE OF A PROTEIN WITH A CUPIN-LIKE FOLD AND UNKNOWN FUNCTION (BXE_C0505) FROM BURKHOLDERIA XENOVORANS LB400 AT 1.55 A RESOLUTION
- PDB DOI: https://doi.org/10.2210/pdb2O8Q/pdb
- Classification: METAL BINDING PROTEIN
- Organism(s): Paraburkholderia xenovorans LB400
- Expression System: Escherichia coli
- Mutation(s): Yes
- Deposited: 2006-12-12 Released: 2006-12-26
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.55 Å
- R-Value Free: 0.191
- R-Value Work: 0.170
- R-Value Observed: 0.171
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:
(by identity cutoff) | 3D Structure
Entity ID: 1 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Hypothetical protein | 134 | Paraburkholderia xenovorans LB400 | Mutation(s): 3 Gene Names: YP_555756.1 |  | |
UniProt | |||||
Find proteins for Q13HN3 (Paraburkholderia xenovorans (strain LB400)) Explore Q13HN3 Go to UniProtKB: Q13HN3 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | Q13HN3 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Small Molecules
| Ligands 2 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| EDO Query on EDO | D [auth A] E [auth A] F [auth A] G [auth A] I [auth B] | 1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N |  | ||
| NI Query on NI | C [auth A], H [auth B] | NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N |  | ||
| Modified Residues 1 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Type | Formula | 2D Diagram | Parent |
| MSE Query on MSE | A, B | L-PEPTIDE LINKING | C5 H11 N O2 Se |  | MET |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 1.55 Å
- R-Value Free: 0.191
- R-Value Work: 0.170
- R-Value Observed: 0.171
- Space Group: P 42 21 2
- Diffraction Data: https://doi.org/10.18430/M32O8Q
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 102.255 | α = 90 |
| b = 102.255 | β = 90 |
| c = 74.746 | γ = 90 |
| Software Name | Purpose |
|---|---|
| MolProbity | model building |
| SHELX | phasing |
| REFMAC | refinement |
| SCALA | data scaling |
| PDB_EXTRACT | data extraction |
| MOSFLM | data reduction |
| CCP4 | data scaling |
| SHELXD | phasing |
| SOLVE | phasing |
Entry History
Deposition Data
- Released Date: 2006-12-26 Deposition Author(s): Joint Center for Structural Genomics (JCSG)
Revision History (Full details and data files)
- Version 1.0: 2006-12-26
Type: Initial release - Version 1.1: 2008-05-01
Changes: Version format compliance - Version 1.2: 2011-07-13
Changes: Advisory, Derived calculations, Source and taxonomy, Version format compliance - Version 1.3: 2017-10-18
Changes: Refinement description - Version 1.4: 2017-10-25
Changes: Author supporting evidence - Version 1.5: 2023-01-25
Changes: Database references, Derived calculations
