Download MendeleyCrystal structure of prokaryotic domain of unknown function (DUF849) with a TIM barrel fold (YP_164873.1) from Silicibacter pomeroyi DSS-3 at 1.45 A resolution
Joint Center for Structural Genomics (JCSG)To be published.
3CHV | pdb_00003chv
CRYSTAL STRUCTURE OF a prokaryotic domain of unknown function (DUF849) member (SPOA0042) FROM SILICIBACTER POMEROYI DSS-3 AT 1.45 A RESOLUTION
- PDB DOI: https://doi.org/10.2210/pdb3CHV/pdb
- Classification: METAL BINDING PROTEIN
- Organism(s): Ruegeria pomeroyi DSS-3
- Expression System: Escherichia coli
- Mutation(s): No
- Deposited: 2008-03-10 Released: 2008-04-01
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.45 Å
- R-Value Free: 0.158 (Depositor), 0.170 (DCC)
- R-Value Work: 0.133 (Depositor), 0.140 (DCC)
- R-Value Observed: 0.134 (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 |
| Prokaryotic domain of unknown function (DUF849) with a TIM barrel fold | 284 | Ruegeria pomeroyi DSS-3 | Mutation(s): 0 Gene Names: YP_164873.1, SPOA0042 |  | |
UniProt | |||||
Find proteins for Q6SJB6 (Ruegeria pomeroyi) Explore Q6SJB6 Go to UniProtKB: Q6SJB6 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | Q6SJB6 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Small Molecules
| Ligands 2 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| ZN Query on ZN | B [auth A], C [auth A] | ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N |  | ||
| CL Query on CL | D [auth A], E [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: 1.45 Å
- R-Value Free: 0.158 (Depositor), 0.170 (DCC)
- R-Value Work: 0.133 (Depositor), 0.140 (DCC)
- R-Value Observed: 0.134 (Depositor)
Diffraction Data: https://doi.org/10.18430/M33CHV
Space Group: C 1 2 1
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 68.859 | α = 90 |
| b = 69.601 | β = 94.19 |
| c = 52.331 | γ = 90 |
| Software Name | Purpose |
|---|---|
| REFMAC | refinement |
| PHENIX | refinement |
| SHELX | phasing |
| MolProbity | model building |
| SCALA | data scaling |
| PDB_EXTRACT | data extraction |
| MAR345 | data collection |
| MOSFLM | data reduction |
| SHELXD | phasing |
| autoSHARP | phasing |
Entry History
Deposition Data
- Released Date: 2008-04-01 Deposition Author(s): Joint Center for Structural Genomics (JCSG)
Revision History (Full details and data files)
- Version 1.0: 2008-04-01
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
