Download MendeleyCrystal structure of Diaminopimelate decarboxylase from Brucella melitensis bound to PLP
Edwards, T.E., Gardberg, A.S., Letesson, J.J., Seattle Structural Genomics Center for Infectious Disease (SSGCID)To be published.
3VAB
Crystal structure of Diaminopimelate decarboxylase from Brucella melitensis bound to PLP
- PDB DOI: https://doi.org/10.2210/pdb3VAB/pdb
- Classification: LYASE
- Organism(s): Brucella melitensis bv. 1 str. 16M
- Expression System: Escherichia coli
- Mutation(s): No
- Deposited: 2011-12-29 Released: 2012-01-18
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.10 Å
- R-Value Free: 0.268
- R-Value Work: 0.221
- R-Value Observed: 0.224
wwPDB Validation 3D Report Full Report
This is version 1.2 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 |
| Diaminopimelate decarboxylase 1 | 443 | Brucella melitensis bv. 1 str. 16M | Mutation(s): 0 Gene Names: BMEI0084, lysA1 EC: 4.1.1.20 |  | |
UniProt | |||||
Find proteins for Q8YJJ9 (Brucella melitensis biotype 1 (strain 16M / ATCC 23456 / NCTC 10094)) Explore Q8YJJ9 Go to UniProtKB: Q8YJJ9 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | Q8YJJ9 | ||||
Sequence AnnotationsExpand | |||||
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Small Molecules
| Ligands 2 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| SO4 Query on SO4 | C [auth A] | SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L |  | ||
| EDO Query on EDO | D [auth A], E [auth A], F [auth B] | 1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N |  | ||
| Modified Residues 1 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Type | Formula | 2D Diagram | Parent |
| LLP Query on LLP | A, B | L-PEPTIDE LINKING | C14 H22 N3 O7 P |  | LYS |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.10 Å
- R-Value Free: 0.268
- R-Value Work: 0.221
- R-Value Observed: 0.224
- Space Group: P 1 21 1
- Diffraction Data: https://doi.org/10.18430/M33VAB
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 59.53 | α = 90 |
| b = 126.37 | β = 112.71 |
| c = 68.18 | γ = 90 |
| Software Name | Purpose |
|---|---|
| XSCALE | data scaling |
| PHASER | phasing |
| REFMAC | refinement |
| PDB_EXTRACT | data extraction |
| StructureStudio | data collection |
| XDS | data reduction |
Entry History
Deposition Data
- Released Date: 2012-01-18 Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)
Revision History (Full details and data files)
- Version 1.0: 2012-01-18
Type: Initial release - Version 1.1: 2023-09-13
Changes: Data collection, Database references, Derived calculations, Refinement description - Version 1.2: 2023-12-06
Changes: Data collection
