3VNZ
Crystal structure of beta-glucuronidase from Acidobacterium capsulatum in complex with D-glucuronic acid
- PDB DOI: https://doi.org/10.2210/pdb3VNZ/pdb
- Classification: HYDROLASE
- Organism(s): Acidobacterium capsulatum ATCC 51196
- Expression System: Escherichia coli
- Mutation(s): No 
- Deposited: 2012-01-18 Released: 2012-02-22 
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.80 Å
- R-Value Free: 0.230 
- R-Value Work: 0.199 
- R-Value Observed: 0.201 
This is version 1.3 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 |
beta-GLUCURONIDASE | 488 | Acidobacterium capsulatum ATCC 51196 | Mutation(s): 0  Gene Names: ACP_2665 EC: 3.2.1.31 | ||
UniProt | |||||
Find proteins for C1F2K5 (Acidobacterium capsulatum (strain ATCC 51196 / DSM 11244 / BCRC 80197 / JCM 7670 / NBRC 15755 / NCIMB 13165 / 161)) Explore C1F2K5  Go to UniProtKB:  C1F2K5 | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | C1F2K5 | ||||
Sequence AnnotationsExpand | |||||
|
Small Molecules
Ligands 3 Unique | |||||
---|---|---|---|---|---|
ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
BDP Query on BDP | B [auth A] | beta-D-glucopyranuronic acid C6 H10 O7 AEMOLEFTQBMNLQ-QIUUJYRFSA-N | |||
PO4 Query on PO4 | C [auth A] | PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K | |||
GOL Query on GOL | D [auth A] | GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 1.80 Å
- R-Value Free: 0.230 
- R-Value Work: 0.199 
- R-Value Observed: 0.201 
- Space Group: I 41 2 2
Unit Cell:
Length ( Å ) | Angle ( ˚ ) |
---|---|
a = 101.271 | α = 90 |
b = 101.271 | β = 90 |
c = 217.768 | γ = 90 |
Software Name | Purpose |
---|---|
ADSC | data collection |
REFMAC | refinement |
HKL-2000 | data reduction |
HKL-2000 | data scaling |
REFMAC | phasing |
Entry History 
Deposition Data
- Released Date: 2012-02-22  Deposition Author(s): Momma, M., Fujimoto, Z., Michikawa, M., Ichinose, H., Yoshida, M., Kotake, Y., Biely, P., Tsumuraya, Y., Kaneko, S.
Revision History (Full details and data files)
- Version 1.0: 2012-02-22
Type: Initial release - Version 1.1: 2015-08-19
Changes: Database references - Version 1.2: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Data collection, Database references, Derived calculations, Structure summary - Version 1.3: 2023-11-08
Changes: Data collection, Database references, Refinement description, Structure summary