Download MendeleyCrystal Structure of SPAP, an alkaline phosphatase from Sphingomonas showing covalent intermediate
Bihani, S.C.To be published.
5XWI
Crystal Structure of SPAP, an alkaline phosphatase from Sphingomonas showing covalent intermediate
- PDB DOI: https://doi.org/10.2210/pdb5XWI/pdb
- Classification: HYDROLASE
- Organism(s): Sphingomonas sp.
- Expression System: Escherichia coli BL21(DE3)
- Mutation(s): No
- Deposited: 2017-06-29 Released: 2018-07-04
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.87 Å
- R-Value Free: 0.210
- R-Value Work: 0.172
- R-Value Observed: 0.173
wwPDB Validation 3D Report Full Report
This is version 1.1 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 |
| Alkaline phosphatase PhoK | 567 | Sphingomonas sp. | Mutation(s): 0 Gene Names: phoK EC: 3.1.3.1 |  | |
UniProt | |||||
Find proteins for A1YYW7 (Sphingomonas sp) Explore A1YYW7 Go to UniProtKB: A1YYW7 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | A1YYW7 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Small Molecules
| Ligands 4 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| SO4 Query on SO4 | F [auth A] | SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L |  | ||
| GOL Query on GOL | E [auth A] | GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N |  | ||
| ZN (Subject of Investigation/LOI) Query on ZN | B [auth A], C [auth A] | ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N |  | ||
| CA Query on CA | D [auth A] | CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N |  | ||
| Modified Residues 1 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Type | Formula | 2D Diagram | Parent |
| TPO Query on TPO | A | L-PEPTIDE LINKING | C4 H10 N O6 P |  | THR |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 1.87 Å
- R-Value Free: 0.210
- R-Value Work: 0.172
- R-Value Observed: 0.173
- Space Group: P 41 21 2
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 87.6 | α = 90 |
| b = 87.6 | β = 90 |
| c = 168.03 | γ = 90 |
| Software Name | Purpose |
|---|---|
| PHENIX | refinement |
| XDS | data reduction |
| XSCALE | data scaling |
| PHASER | phasing |
Entry History
Deposition Data
- Released Date: 2018-07-04 Deposition Author(s): Bihani, S.C.
Revision History (Full details and data files)
- Version 1.0: 2018-07-04
Type: Initial release - Version 1.1: 2023-11-22
Changes: Data collection, Database references, Derived calculations, Refinement description
