Download MendeleyA two-domain structure of alkaliphilic XynJ from Bacillus sp. 41M-1
Ihsanawati, Tanaka, N., Nakamura, S., Kumasaka, T.To be published.
2DCK | pdb_00002dck
A tetragonal-lattice structure of alkaliphilic XynJ from Bacillus sp. 41M-1
- PDB DOI: https://doi.org/10.2210/pdb2DCK/pdb
- Classification: HYDROLASE
- Organism(s): Bacillus sp. 41M-1
- Expression System: Escherichia coli
- Mutation(s): No
- Deposited: 2006-01-07 Released: 2007-03-20
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.10 Å
- R-Value Free: 0.198 (Depositor), 0.190 (DCC)
- R-Value Work: 0.167 (Depositor), 0.180 (DCC)
- R-Value Observed: 0.168 (Depositor)
Starting Model: experimental
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wwPDB Validation 3D Report Full Report
This is version 1.3 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 |
| xylanase J | 354 | Bacillus sp. 41M-1 | Mutation(s): 0 Gene Names: xynJ EC: 3.2.1.8 |  | |
UniProt | |||||
Find proteins for Q9RC94 (Bacillus sp. 41M-1) Explore Q9RC94 Go to UniProtKB: Q9RC94 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | Q9RC94 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Small Molecules
| Ligands 2 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| GOL Query on GOL | D [auth A], E [auth A], F [auth A], G [auth A] | GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N |  | ||
| CA Query on CA | B [auth A], C [auth A] | CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N |  | ||
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.10 Å
- R-Value Free: 0.198 (Depositor), 0.190 (DCC)
- R-Value Work: 0.167 (Depositor), 0.180 (DCC)
- R-Value Observed: 0.168 (Depositor)
Space Group: P 43
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 116.579 | α = 90 |
| b = 116.579 | β = 90 |
| c = 45.909 | γ = 90 |
| Software Name | Purpose |
|---|---|
| REFMAC | refinement |
| HKL-2000 | data reduction |
| SCALEPACK | data scaling |
| MOLREP | phasing |
Entry History
Deposition Data
- Released Date: 2007-03-20 Deposition Author(s): Fibriansah, G., Ihsanawati, Tanaka, N., Nakamura, S., Kumasaka, T.
Revision History (Full details and data files)
- Version 1.0: 2007-03-20
Type: Initial release - Version 1.1: 2008-04-30
Changes: Version format compliance - Version 1.2: 2011-07-13
Changes: Source and taxonomy, Version format compliance - Version 1.3: 2023-10-25
Changes: Data collection, Database references, Derived calculations, Refinement description
