Download MendeleyCrystal structure of Putative pectinase (YP_001304412.1) from Parabacteroides distasonis ATCC 8503 at 2.30 A resolution
Joint Center for Structural Genomics (JCSG)To be published.
3LYC | pdb_00003lyc
Crystal structure of Putative pectinase (YP_001304412.1) from Parabacteroides distasonis ATCC 8503 at 2.30 A resolution
- PDB DOI: https://doi.org/10.2210/pdb3LYC/pdb
- Classification: CELL ADHESION
- Organism(s): Parabacteroides distasonis ATCC 8503
- Expression System: Escherichia coli
- Mutation(s): No
- Deposited: 2010-02-26 Released: 2010-03-16
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.30 Å
- R-Value Free: 0.280 (Depositor), 0.290 (DCC)
- R-Value Work: 0.244 (Depositor), 0.250 (DCC)
- R-Value Observed: 0.246 (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 pectinase | 241 | Parabacteroides distasonis ATCC 8503 | Mutation(s): 0 Gene Names: BDI_3084 |  | |
UniProt | |||||
Find proteins for A6LGH6 (Parabacteroides distasonis (strain ATCC 8503 / DSM 20701 / CIP 104284 / JCM 5825 / NCTC 11152)) Explore A6LGH6 Go to UniProtKB: A6LGH6 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | A6LGH6 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Small Molecules
| Modified Residues 1 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Type | Formula | 2D Diagram | Parent |
| MSE Query on MSE | A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P | L-PEPTIDE LINKING | C5 H11 N O2 Se |  | MET |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.30 Å
- R-Value Free: 0.280 (Depositor), 0.290 (DCC)
- R-Value Work: 0.244 (Depositor), 0.250 (DCC)
- R-Value Observed: 0.246 (Depositor)
Diffraction Data: https://doi.org/10.18430/M33LYC
Space Group: P 21 21 21
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 104.116 | α = 90 |
| b = 104.606 | β = 90 |
| c = 393.587 | 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: 2010-03-16 Deposition Author(s): Joint Center for Structural Genomics (JCSG)
Revision History (Full details and data files)
- Version 1.0: 2010-03-16
Type: Initial release - Version 1.1: 2011-07-13
Changes: Advisory, Version format compliance - Version 1.2: 2017-11-08
Changes: Refinement description - Version 1.3: 2019-07-17
Changes: Data collection, Derived calculations, Refinement description - Version 1.4: 2023-02-01
Changes: Database references - Version 1.5: 2024-11-06
Changes: Data collection, Refinement description, Structure summary
