4W86
Crystal structure of XEG5A, a GH5 xyloglucan-specific endo-beta-1,4-glucanase from ruminal metagenomic library, in complex with glucose and TRIS
- PDB DOI: https://doi.org/10.2210/pdb4W86/pdb
- Classification: HYDROLASE
- Organism(s): uncultured bacterium
- Expression System: Escherichia coli
- Mutation(s): Yes 
- Deposited: 2014-08-22 Released: 2015-03-11 
- Funding Organization(s): Sao Paulo Research Foundation (FAPESP)
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.64 Å
- R-Value Free: 0.236 
- R-Value Work: 0.214 
- R-Value Observed: 0.216 
This is version 1.6 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 |
Xyloglucan-specific endo-beta-1,4-glucanase | 339 | uncultured bacterium | Mutation(s): 1  EC: 3.2.1.151 | ||
UniProt | |||||
Find proteins for D2K7Z0 (uncultured bacterium) Explore D2K7Z0  Go to UniProtKB:  D2K7Z0 | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | D2K7Z0 | ||||
Sequence AnnotationsExpand | |||||
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Small Molecules
Ligands 3 Unique | |||||
---|---|---|---|---|---|
ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
BGC Query on BGC | D [auth A], G [auth B] | beta-D-glucopyranose C6 H12 O6 WQZGKKKJIJFFOK-VFUOTHLCSA-N | |||
TRS Query on TRS | C [auth A], F [auth B] | 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C4 H12 N O3 LENZDBCJOHFCAS-UHFFFAOYSA-O | |||
MG Query on MG | E [auth A], H [auth B] | MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N |
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: 2.64 Å
- R-Value Free: 0.236 
- R-Value Work: 0.214 
- R-Value Observed: 0.216 
- Space Group: P 31
Unit Cell:
Length ( Å ) | Angle ( ˚ ) |
---|---|
a = 96.95 | α = 90 |
b = 96.95 | β = 90 |
c = 95.785 | γ = 120 |
Software Name | Purpose |
---|---|
XDS | data scaling |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
MOLREP | phasing |
XSCALE | data scaling |
Entry History & Funding Information
Deposition Data
- Released Date: 2015-03-11  Deposition Author(s): Santos, C.R., Cordeiro, R.L., Wong, D.W.S., Murakami, M.T.
Funding Organization | Location | Grant Number |
---|---|---|
Sao Paulo Research Foundation (FAPESP) | Brazil | 2013/13309-0, 2014/07135-1 |
Revision History (Full details and data files)
- Version 1.0: 2015-03-11
Type: Initial release - Version 1.1: 2015-03-25
Changes: Database references - Version 1.2: 2017-11-22
Changes: Database references, Derived calculations, Other, Refinement description, Source and taxonomy, Structure summary - Version 1.3: 2019-04-17
Changes: Author supporting evidence, Data collection - Version 1.4: 2020-01-01
Changes: Author supporting evidence, Data collection - Version 1.5: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Data collection, Derived calculations, Refinement description, Structure summary - Version 1.6: 2023-12-27
Changes: Data collection, Database references, Structure summary