Download MendeleyCrystal structures reveal metal-binding plasticity at the active site of PqqB
Tu, X., Wilmot, C.M.To be published.
4Z5Z
The 2.5-angstrom crystal structure of Mg(2+)-bound PqqB from Pseudomonas Putida
- PDB DOI: https://doi.org/10.2210/pdb4Z5Z/pdb
- Classification: HYDROLASE
- Organism(s): Pseudomonas putida KT2440
- Expression System: Escherichia coli BL21(DE3)
- Mutation(s): No
- Deposited: 2015-04-03 Released: 2016-04-13
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.54 Å
- R-Value Free: 0.224
- R-Value Work: 0.188
- R-Value Observed: 0.190
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 |
| Coenzyme PQQ synthesis protein B | 308 | Pseudomonas putida KT2440 | Mutation(s): 0 Gene Names: pqqB, PP_0379 |  | |
UniProt | |||||
Find proteins for Q88QV5 (Pseudomonas putida (strain ATCC 47054 / DSM 6125 / CFBP 8728 / NCIMB 11950 / KT2440)) Explore Q88QV5 Go to UniProtKB: Q88QV5 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | Q88QV5 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Small Molecules
| Ligands 3 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| MLT Query on MLT | D [auth A] | D-MALATE C4 H6 O5 BJEPYKJPYRNKOW-UWTATZPHSA-N |  | ||
| ZN Query on ZN | B [auth A] | ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N |  | ||
| MG Query on MG | C [auth A] | MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N |  | ||
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.54 Å
- R-Value Free: 0.224
- R-Value Work: 0.188
- R-Value Observed: 0.190
- Space Group: P 43 21 2
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 86.15 | α = 90 |
| b = 86.15 | β = 90 |
| c = 106.959 | γ = 90 |
| Software Name | Purpose |
|---|---|
| SCALEPACK | data scaling |
| PHASER | phasing |
| PHENIX | refinement |
| PDB_EXTRACT | data extraction |
| HKL-3000 | data reduction |
Entry History
Deposition Data
- Released Date: 2016-04-13 Deposition Author(s): Tu, X., Wilmot, C.M.
Revision History (Full details and data files)
- Version 1.0: 2016-04-13
Type: Initial release - Version 1.1: 2024-03-06
Changes: Data collection, Database references, Derived calculations
