Download MendeleyCrystal structure of Putative metallopeptidase (YP_001051774.1) from SHEWANELLA BALTICA OS155 at 2.45 A resolution
Joint Center for Structural Genomics (JCSG)To be published.
3IEH | pdb_00003ieh
Crystal structure of Putative metallopeptidase (YP_001051774.1) from SHEWANELLA BALTICA OS155 at 2.45 A resolution
- PDB DOI: https://doi.org/10.2210/pdb3IEH/pdb
- Classification: HYDROLASE
- Organism(s): Shewanella baltica OS155
- Expression System: Escherichia coli
- Mutation(s): No
- Deposited: 2009-07-22 Released: 2009-08-04
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.45 Å
- R-Value Free: 0.222 (Depositor), 0.220 (DCC)
- R-Value Work: 0.164 (Depositor), 0.170 (DCC)
- R-Value Observed: 0.167 (Depositor)
wwPDB Validation 3D Report Full Report
This is version 1.5 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 |
| Putative metallopeptidase | 276 | Shewanella baltica OS155 | Mutation(s): 0 Gene Names: Sbal_3428, YP_001051774.1 |  | |
UniProt | |||||
Find proteins for A3D842 (Shewanella baltica (strain OS155 / ATCC BAA-1091)) Explore A3D842 Go to UniProtKB: A3D842 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | A3D842 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Small Molecules
| Ligands 5 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| PGE Query on PGE | M [auth A], N [auth A] | TRIETHYLENE GLYCOL C6 H14 O4 ZIBGPFATKBEMQZ-UHFFFAOYSA-N |  | ||
| PEG Query on PEG | J [auth A], K [auth A], L [auth A] | DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N |  | ||
| GOL Query on GOL | D [auth A] E [auth A] F [auth A] G [auth A] H [auth A] | GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N |  | ||
| ZN Query on ZN | B [auth A] | ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N |  | ||
| UNL Query on UNL | C [auth A] | Unknown ligand PTFCDOFLOPIGGS-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: 2.45 Å
- R-Value Free: 0.222 (Depositor), 0.220 (DCC)
- R-Value Work: 0.164 (Depositor), 0.170 (DCC)
- R-Value Observed: 0.167 (Depositor)
Diffraction Data: https://doi.org/10.18430/M33IEH
Space Group: P 65
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 80.958 | α = 90 |
| b = 80.958 | β = 90 |
| c = 87.94 | γ = 120 |
| Software Name | Purpose |
|---|---|
| REFMAC | refinement |
| PHENIX | refinement |
| SHELX | phasing |
| MolProbity | model building |
| SCALA | data scaling |
| PDB_EXTRACT | data extraction |
| MOSFLM | data reduction |
| SHARP | phasing |
Entry History
Deposition Data
- Released Date: 2009-08-04 Deposition Author(s): Joint Center for Structural Genomics (JCSG)
Revision History (Full details and data files)
- Version 1.0: 2009-08-04
Type: Initial release - Version 1.1: 2011-07-13
Changes: Advisory, Version format compliance - Version 1.2: 2017-10-25
Changes: Author supporting evidence, Refinement description - Version 1.3: 2019-07-24
Changes: Data collection, Derived calculations, Refinement description - Version 1.4: 2023-02-01
Changes: Database references, Derived calculations - Version 1.5: 2024-11-20
Changes: Data collection, Structure summary
