Download MendeleyCrystal structure of a pyrophosphatase (AF1178) from Archaeoglobus fulgidus DSM 4304 at 1.80 A resolution
Joint Center for Structural Genomics (JCSG)To be published.
4QGP
Crystal structure of a pyrophosphatase (AF1178) from Archaeoglobus fulgidus DSM 4304 at 1.80 A resolution
- PDB DOI: https://doi.org/10.2210/pdb4QGP/pdb
- Entry: 4QGP supersedes: 3OBC
- Classification: HYDROLASE
- Organism(s): Archaeoglobus fulgidus DSM 4304
- Expression System: Escherichia coli
- Mutation(s): No
- Deposited: 2014-05-23 Released: 2014-07-02
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.78 Å
- R-Value Free: 0.238
- R-Value Work: 0.194
- R-Value Observed: 0.196
wwPDB Validation 3D Report Full Report
This is version 1.3 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 |
| pyrophosphatase | 118 | Archaeoglobus fulgidus DSM 4304 | Mutation(s): 0 Gene Names: AF_1178 |  | |
UniProt | |||||
Find proteins for O29089 (Archaeoglobus fulgidus (strain ATCC 49558 / DSM 4304 / JCM 9628 / NBRC 100126 / VC-16)) Explore O29089 Go to UniProtKB: O29089 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | O29089 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Small Molecules
| Ligands 5 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| PG4 Query on PG4 | F [auth B] | TETRAETHYLENE GLYCOL C8 H18 O5 UWHCKJMYHZGTIT-UHFFFAOYSA-N |  | ||
| PGE Query on PGE | G [auth B] | TRIETHYLENE GLYCOL C6 H14 O4 ZIBGPFATKBEMQZ-UHFFFAOYSA-N |  | ||
| CL Query on CL | D [auth A] | CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M |  | ||
| MG Query on MG | C [auth A], E [auth B] | MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N |  | ||
| NA Query on NA | H [auth B], I [auth B] | SODIUM ION Na FKNQFGJONOIPTF-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: 1.78 Å
- R-Value Free: 0.238
- R-Value Work: 0.194
- R-Value Observed: 0.196
- Space Group: I 21 21 21
- Diffraction Data: https://doi.org/10.18430/M34QGP
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 49.168 | α = 90 |
| b = 102.136 | β = 90 |
| c = 103.285 | γ = 90 |
| Software Name | Purpose |
|---|---|
| MolProbity | model building |
| PDB_EXTRACT | data extraction |
| SHELX | phasing |
| SHARP | phasing |
| XSCALE | data scaling |
| REFMAC | refinement |
| XDS | data reduction |
| SHELXD | phasing |
Entry History
Deposition Data
- Released Date: 2014-07-02 Deposition Author(s): Joint Center for Structural Genomics (JCSG)
- This entry supersedes: 3OBC
Revision History (Full details and data files)
- Version 1.0: 2014-07-02
Type: Initial release - Version 1.1: 2017-11-22
Changes: Refinement description - Version 1.2: 2018-01-24
Changes: Database references - Version 1.3: 2024-11-06
Changes: Data collection, Database references, Derived calculations, Structure summary
