2Z8S
Crystal structure of rhamnogalacturonan lyase YesW complexed with digalacturonic acid
- PDB DOI: https://doi.org/10.2210/pdb2Z8S/pdb
- Classification: LYASE
- Organism(s): Bacillus subtilis
- Expression System: Escherichia coli
- Mutation(s): No 
- Deposited: 2007-09-10 Released: 2007-10-16 
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.50 Å
- R-Value Free: 0.242 
- R-Value Work: 0.162 
- R-Value Observed: 0.166 
wwPDB Validation   3D Report Full Report
This is version 2.1 of the entry. See complete history. 
Macromolecules
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 1 | |||||
---|---|---|---|---|---|
Molecule | Chains | Sequence Length | Organism | Details | Image |
YesW protein | 591 | Bacillus subtilis | Mutation(s): 0  Gene Names: yesW EC: 4.2.2 | ||
UniProt | |||||
Find proteins for O31526 (Bacillus subtilis (strain 168)) Explore O31526  Go to UniProtKB:  O31526 | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | O31526 | ||||
Sequence AnnotationsExpand | |||||
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Oligosaccharides
Small Molecules
Ligands 1 Unique | |||||
---|---|---|---|---|---|
ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
CA Query on CA | E [auth A] F [auth A] G [auth A] H [auth A] I [auth A] | CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.50 Å
- R-Value Free: 0.242 
- R-Value Work: 0.162 
- R-Value Observed: 0.166 
- Space Group: P 1 21 1
Unit Cell:
Length ( Å ) | Angle ( ˚ ) |
---|---|
a = 56.617 | α = 90 |
b = 105.152 | β = 95.22 |
c = 100.668 | γ = 90 |
Software Name | Purpose |
---|---|
REFMAC | refinement |
SADIE | data collection |
SAINT | data reduction |
SAINT | data scaling |
MOLREP | phasing |
Entry History 
Deposition Data
- Released Date: 2007-10-16  Deposition Author(s): Ochiai, A., Itoh, T., Maruyama, Y., Kawamata, A., Mikami, B., Hashimoto, W., Murata, K.
Revision History (Full details and data files)
- Version 1.0: 2007-10-16
Type: Initial release - Version 1.1: 2011-07-13
Changes: Version format compliance - Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Database references, Derived calculations, Structure summary - Version 2.1: 2023-11-01
Changes: Data collection, Database references, Refinement description, Structure summary