Download MendeleyCrystal structure of protein of unknown function (DUF1989) (YP_165628.1) from SILICIBACTER POMEROYI DSS-3 at 1.60 A resolution
Joint Center for Structural Genomics (JCSG)To be published.
3DI4 | pdb_00003di4
Crystal structure of a duf1989 family protein (spo0365) from silicibacter pomeroyi dss-3 at 1.60 A resolution
- PDB DOI: https://doi.org/10.2210/pdb3DI4/pdb
- Classification: METAL BINDING PROTEIN
- Organism(s): Ruegeria pomeroyi DSS-3
- Expression System: Escherichia coli
- Mutation(s): No
- Deposited: 2008-06-19 Released: 2008-07-01
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.60 Å
- R-Value Free: 0.175 (Depositor), 0.180 (DCC)
- R-Value Work: 0.141 (Depositor), 0.150 (DCC)
- R-Value Observed: 0.142 (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:
(by identity cutoff) | 3D Structure
Entity ID: 1 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Uncharacterized Protein DUF1989 | 286 | Ruegeria pomeroyi DSS-3 | Mutation(s): 0 Gene Names: YP_165628.1, SPO0365 |  | |
UniProt | |||||
Find proteins for Q5LXE3 (Ruegeria pomeroyi (strain ATCC 700808 / DSM 15171 / DSS-3)) Explore Q5LXE3 Go to UniProtKB: Q5LXE3 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | Q5LXE3 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Small Molecules
| Ligands 4 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| SO4 Query on SO4 | H [auth B] | SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L |  | ||
| GOL Query on GOL | F [auth A] | GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N |  | ||
| ZN Query on ZN | C [auth A], G [auth B] | ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N |  | ||
| CL Query on CL | D [auth A], E [auth A], I [auth B], J [auth B] | CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M |  | ||
| 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: 1.60 Å
- R-Value Free: 0.175 (Depositor), 0.180 (DCC)
- R-Value Work: 0.141 (Depositor), 0.150 (DCC)
- R-Value Observed: 0.142 (Depositor)
Diffraction Data: https://doi.org/10.18430/M33DI4
Space Group: P 1 21 1
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 51.465 | α = 90 |
| b = 95.764 | β = 109.04 |
| c = 58.689 | γ = 90 |
| Software Name | Purpose |
|---|---|
| REFMAC | refinement |
| PHENIX | refinement |
| SHELX | phasing |
| MolProbity | model building |
| SCALA | data scaling |
| PDB_EXTRACT | data extraction |
| MOSFLM | data reduction |
| SHELXD | phasing |
| autoSHARP | phasing |
Entry History
Deposition Data
- Released Date: 2008-07-01 Deposition Author(s): Joint Center for Structural Genomics (JCSG)
Revision History (Full details and data files)
- Version 1.0: 2008-07-01
Type: Initial release - Version 1.1: 2011-07-13
Changes: Source and taxonomy, 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: 2024-10-09
Changes: Data collection, Refinement description, Structure summary
