4PMY
Crystal structure of GH10 endo-b-1,4-xylanase (XynB) from Xanthomonas axonopodis pv citri complexed with xylose
- PDB DOI: https://doi.org/10.2210/pdb4PMY/pdb
- Classification: HYDROLASE
- Organism(s): Xanthomonas citri pv. citri str. 306
- Expression System: Escherichia coli
- Mutation(s): No 
- Deposited: 2014-05-22 Released: 2014-10-08 
- Funding Organization(s): Sao Paulo Research Foundation (FAPESP)
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.60 Å
- R-Value Free: 0.227 
- R-Value Work: 0.186 
- R-Value Observed: 0.188 
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 |
Xylanase | 303 | Xanthomonas citri pv. citri str. 306 | Mutation(s): 0  Gene Names: xynB, XAC4254 | ||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
Sequence AnnotationsExpand | |||||
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Small Molecules
Ligands 3 Unique | |||||
---|---|---|---|---|---|
ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
XYP Query on XYP | C [auth A], F [auth B] | beta-D-xylopyranose C5 H10 O5 SRBFZHDQGSBBOR-KKQCNMDGSA-N | |||
GOL Query on GOL | D [auth A], G [auth B] | GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N | |||
CA Query on CA | E [auth A], H [auth B] | CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 1.60 Å
- R-Value Free: 0.227 
- R-Value Work: 0.186 
- R-Value Observed: 0.188 
- Space Group: P 1 21 1
Unit Cell:
Length ( Å ) | Angle ( ˚ ) |
---|---|
a = 71.866 | α = 90 |
b = 48.201 | β = 90.12 |
c = 77.798 | γ = 90 |
Software Name | Purpose |
---|---|
XDS | data reduction |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
Entry History & Funding Information
Deposition Data
- Released Date: 2014-10-08  Deposition Author(s): Santos, C.R., Martins, V.P.M., Zanphorlin, L.M., Ruller, R., Murakami, M.T.
Funding Organization | Location | Grant Number |
---|---|---|
Sao Paulo Research Foundation (FAPESP) | Brazil | 13/13309-0 |
Revision History (Full details and data files)
- Version 1.0: 2014-10-08
Type: Initial release - Version 1.1: 2014-10-15
Changes: Database references, Structure summary - Version 1.2: 2014-11-26
Changes: Database references - Version 1.3: 2015-02-04
Changes: Derived calculations - Version 1.4: 2019-04-17
Changes: Author supporting evidence, Data collection, Database references, Derived calculations, Other, Source and taxonomy, Structure summary - Version 1.5: 2020-01-01
Changes: Author supporting evidence - Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Derived calculations, Refinement description, Structure summary - Version 2.1: 2023-12-27
Changes: Data collection, Database references, Structure summary