Download MendeleyCrystal structure of protein of unknown function (DUF849) (YP_917261.1) from PARACOCCUS DENITRIFICANS PD1222 at 1.90 A resolution
Joint Center for Structural Genomics (JCSG)To be published.
3FA5
CRYSTAL STRUCTURE OF a DUF849 family protein (PDEN_3495) FROM PARACOCCUS DENITRIFICANS PD1222 AT 1.90 A RESOLUTION
- PDB DOI: https://doi.org/10.2210/pdb3FA5/pdb
- Classification: METAL BINDING PROTEIN
- Organism(s): Paracoccus denitrificans PD1222
- Expression System: Escherichia coli
- Mutation(s): No
- Deposited: 2008-11-14 Released: 2008-12-02
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.90 Å
- R-Value Free: 0.248 (Depositor), 0.250 (DCC)
- R-Value Work: 0.205 (Depositor), 0.210 (DCC)
- R-Value Observed: 0.207 (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 |
| protein of unknown function (DUF849) | 282 | Paracoccus denitrificans PD1222 | Mutation(s): 0 Gene Names: Pden_3495, YP_917261.1 |  | |
UniProt | |||||
Find proteins for A1B7S1 (Paracoccus denitrificans (strain Pd 1222)) Explore A1B7S1 Go to UniProtKB: A1B7S1 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | A1B7S1 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Small Molecules
| Ligands 3 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| EDO Query on EDO | D [auth A] E [auth A] I [auth B] J [auth B] K [auth B] | 1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N |  | ||
| CL Query on CL | F [auth A], G [auth A] | CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M |  | ||
| MG Query on MG | C [auth A], H [auth B] | MAGNESIUM ION Mg JLVVSXFLKOJNIY-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: 1.90 Å
- R-Value Free: 0.248 (Depositor), 0.250 (DCC)
- R-Value Work: 0.205 (Depositor), 0.210 (DCC)
- R-Value Observed: 0.207 (Depositor)
Diffraction Data: https://doi.org/10.18430/M33FA5
Space Group: P 21 21 2
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 92.579 | α = 90 |
| b = 139.567 | β = 90 |
| c = 45.765 | 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: 2008-12-02 Deposition Author(s): Joint Center for Structural Genomics (JCSG)
Revision History (Full details and data files)
- Version 1.0: 2008-12-02
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: 2019-07-24
Changes: Data collection, Derived calculations, Refinement description - Version 1.4: 2023-02-01
Changes: Database references, Derived calculations - Version 1.5: 2024-11-06
Changes: Data collection, Refinement description, Structure summary
