Download MendeleyCrystal structure of putative M16-like peptidase from Alicyclobacillus acidocaldarius
Michalska, K., Tesar, C., Bearden, J., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)To be published.
4XEA
Crystal structure of putative M16-like peptidase from Alicyclobacillus acidocaldarius
- PDB DOI: https://doi.org/10.2210/pdb4XEA/pdb
- Classification: HYDROLASE
- Organism(s): Alicyclobacillus acidocaldarius subsp. acidocaldarius DSM 446
- Expression System: Escherichia coli
- Mutation(s): No
- Deposited: 2014-12-23 Released: 2015-03-18
- Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.95 Å
- R-Value Free: 0.214
- R-Value Work: 0.181
- R-Value Observed: 0.182
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 |
| Peptidase M16 domain protein | 423 | Alicyclobacillus acidocaldarius subsp. acidocaldarius DSM 446 | Mutation(s): 0 Gene Names: Aaci_1020 |  | |
UniProt | |||||
Find proteins for C8WVD6 (Alicyclobacillus acidocaldarius subsp. acidocaldarius (strain ATCC 27009 / DSM 446 / BCRC 14685 / JCM 5260 / KCTC 1825 / NBRC 15652 / NCIMB 11725 / NRRL B-14509 / 104-IA)) Explore C8WVD6 Go to UniProtKB: C8WVD6 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | C8WVD6 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Small Molecules
| Ligands 4 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| GOL Query on GOL | F [auth A], G [auth A] | GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N |  | ||
| ACT Query on ACT | D [auth A], E [auth A] | ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M |  | ||
| NI Query on NI | C [auth A] | NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N |  | ||
| NA Query on NA | B [auth A] | SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N |  | ||
| Modified Residues 1 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Type | Formula | 2D Diagram | Parent |
| MSE Query on MSE | A | L-PEPTIDE LINKING | C5 H11 N O2 Se |  | MET |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 1.95 Å
- R-Value Free: 0.214
- R-Value Work: 0.181
- R-Value Observed: 0.182
- Space Group: P 43 21 2
- Diffraction Data: https://doi.org/10.18430/M34XEA
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 127.201 | α = 90 |
| b = 127.201 | β = 90 |
| c = 65.991 | γ = 90 |
| Software Name | Purpose |
|---|---|
| SBC-Collect | data collection |
| REFMAC | refinement |
| PDB_EXTRACT | data extraction |
| HKL-3000 | data scaling |
| MLPHARE | phasing |
| HKL-3000 | phasing |
| ARP | model building |
| SHELX | phasing |
| DM | phasing |
| HKL-3000 | data reduction |
| WARP | model building |
| SHELX | model building |
| DM | model building |
Entry History & Funding Information
Deposition Data
- Released Date: 2015-03-18 Deposition Author(s): Michalska, K., Tesar, C., Bearden, J., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)
| Funding Organization | Location | Grant Number |
|---|---|---|
| National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) | United States | GM094585 |
Revision History (Full details and data files)
- Version 1.0: 2015-03-18
Type: Initial release - Version 1.1: 2017-09-20
Changes: Author supporting evidence, Derived calculations, Refinement description, Source and taxonomy - Version 1.2: 2019-12-25
Changes: Author supporting evidence
