Download MendeleyCrystal structure of Amidase, hydantoinase/carbamoylase family from Burkholderia vietnamiensis
Abendroth, J., Horanyi, P.S., Lorimer, D.D., Edwards, T.E.To be published.
5I4M | pdb_00005i4m
Crystal structure of Amidase, hydantoinase/carbamoylase family from Burkholderia vietnamiensis
- PDB DOI: https://doi.org/10.2210/pdb5I4M/pdb
- Classification: HYDROLASE
- Organism(s): Burkholderia vietnamiensis G4
- Expression System: Escherichia coli BL21(DE3)
- Mutation(s): No
- Deposited: 2016-02-12 Released: 2016-03-02
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.80 Å
- R-Value Free: 0.171 (Depositor), 0.170 (DCC)
- R-Value Work: 0.139 (Depositor), 0.140 (DCC)
- R-Value Observed: 0.139 (Depositor)
Starting Model: experimental
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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 |
| Amidase, hydantoinase/carbamoylase family | 434 | Burkholderia vietnamiensis G4 | Mutation(s): 0 Gene Names: Bcep1808_5509 EC: 3.5.1.87 |  | |
UniProt | |||||
Find proteins for A4JQA0 (Burkholderia vietnamiensis (strain G4 / LMG 22486)) Explore A4JQA0 Go to UniProtKB: A4JQA0 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | A4JQA0 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Small Molecules
| Ligands 2 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| 3PG Query on 3PG | E [auth A], H [auth B] | 3-PHOSPHOGLYCERIC ACID C3 H7 O7 P OSJPPGNTCRNQQC-UWTATZPHSA-N |  | ||
| ZN Query on ZN | C [auth A], D [auth A], F [auth B], G [auth B] | ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N |  | ||
| Modified Residues 1 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Type | Formula | 2D Diagram | Parent |
| OCS Query on OCS | A, B | L-PEPTIDE LINKING | C3 H7 N O5 S |  | CYS |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 1.80 Å
- R-Value Free: 0.171 (Depositor), 0.170 (DCC)
- R-Value Work: 0.139 (Depositor), 0.140 (DCC)
- R-Value Observed: 0.139 (Depositor)
Diffraction Data: https://doi.org/10.18430/M35I4M
Space Group: P 1 21 1
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 47.46 | α = 90 |
| b = 124.23 | β = 101.94 |
| c = 77.04 | γ = 90 |
| Software Name | Purpose |
|---|---|
| XDS | data reduction |
| XSCALE | data scaling |
| MOLREP | phasing |
| Coot | model building |
| PHENIX | refinement |
| PDB_EXTRACT | data extraction |
Entry History
Deposition Data
- Released Date: 2016-03-02 Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)
Revision History (Full details and data files)
- Version 1.0: 2016-03-02
Type: Initial release - Version 1.1: 2023-09-27
Changes: Data collection, Database references, Derived calculations, Refinement description - Version 1.2: 2023-11-15
Changes: Data collection
