Download MendeleyCrystal structure of protein of unknown function with cystatin-like fold (YP_001022489.1) from METHYLOBIUM PETROLEOPHILUM PM1 at 1.45 A resolution
Joint Center for Structural Genomics (JCSG)To be published.
3G16 | pdb_00003g16
Crystal structure of protein of unknown function with cystatin-like fold (YP_001022489.1) from METHYLOBIUM PETROLEOPHILUM PM1 at 1.45 A resolution
- PDB DOI: https://doi.org/10.2210/pdb3G16/pdb
- Classification: structural genomics, unknown function
- Organism(s): Methylibium petroleiphilum PM1
- Expression System: Escherichia coli
- Mutation(s): No
- Deposited: 2009-01-29 Released: 2009-02-17
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.45 Å
- R-Value Free: 0.167 (Depositor), 0.170 (DCC)
- R-Value Work: 0.148 (Depositor), 0.150 (DCC)
- R-Value Observed: 0.149 (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 |
| uncharacterized protein with cystatin-like fold | 156 | Methylibium petroleiphilum PM1 | Mutation(s): 0 Gene Names: Mpe_A3301, YP_001022489.1 |  | |
UniProt | |||||
Find proteins for A2SL15 (Methylibium petroleiphilum (strain ATCC BAA-1232 / LMG 22953 / PM1)) Explore A2SL15 Go to UniProtKB: A2SL15 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | A2SL15 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Small Molecules
| Ligands 3 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| GOL Query on GOL | G [auth A], H [auth A] | GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N |  | ||
| CL Query on CL | D [auth A], E [auth A], F [auth A], J [auth B] | CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M |  | ||
| UNL Query on UNL | C [auth A], I [auth B] | Unknown ligand VEXZGXHMUGYJMC-UHFFFAOYSA-M | |||
| Modified Residues 1 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Type | Formula | 2D Diagram | Parent |
| MSE Query on MSE | A, B | L-PEPTIDE LINKING | C5 H11 N O2 Se |  | MET |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 1.45 Å
- R-Value Free: 0.167 (Depositor), 0.170 (DCC)
- R-Value Work: 0.148 (Depositor), 0.150 (DCC)
- R-Value Observed: 0.149 (Depositor)
Diffraction Data: https://doi.org/10.18430/M33G16
Space Group: P 21 21 21
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 48.56 | α = 90 |
| b = 68.45 | β = 90 |
| c = 107.46 | γ = 90 |
| Software Name | Purpose |
|---|---|
| REFMAC | refinement |
| PHENIX | refinement |
| SHELX | phasing |
| MolProbity | model building |
| XSCALE | data scaling |
| PDB_EXTRACT | data extraction |
| XDS | data reduction |
| SHELXD | phasing |
| autoSHARP | phasing |
Entry History
Deposition Data
- Released Date: 2009-02-17 Deposition Author(s): Joint Center for Structural Genomics (JCSG)
Revision History (Full details and data files)
- Version 1.0: 2009-02-17
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
