2W5F
High resolution crystallographic structure of the Clostridium thermocellum N-terminal endo-1,4-beta-D-xylanase 10B (Xyn10B) CBM22-1- GH10 modules complexed with xylohexaose
- PDB DOI: https://doi.org/10.2210/pdb2W5F/pdb
- Classification: HYDROLASE
- Organism(s): Acetivibrio thermocellus
- Expression System: Escherichia coli BL21(DE3)
- Mutation(s): Yes 
- Deposited: 2008-12-10 Released: 2010-01-19 
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.90 Å
- R-Value Free: 0.194 
- R-Value Work: 0.164 
- R-Value Observed: 0.166 
wwPDB Validation   3D Report Full Report
This is version 2.0 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 |
ENDO-1,4-BETA-XYLANASE Y | 540 | Acetivibrio thermocellus | Mutation(s): 1  EC: 3.2.1.8 | ||
UniProt | |||||
Find proteins for P51584 (Acetivibrio thermocellus) Explore P51584  Go to UniProtKB:  P51584 | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | P51584 | ||||
Sequence AnnotationsExpand | |||||
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Oligosaccharides
Small Molecules
Ligands 2 Unique | |||||
---|---|---|---|---|---|
ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
CD Query on CD | K [auth A] L [auth A] M [auth A] N [auth A] O [auth A] | CADMIUM ION Cd WLZRMCYVCSSEQC-UHFFFAOYSA-N | |||
ACT Query on ACT | E [auth A] F [auth A] G [auth A] H [auth A] I [auth A] | ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M |
Biologically Interesting Molecules (External Reference) 1 Unique
Entity ID: 2 | |||||
---|---|---|---|---|---|
ID | Chains | Name | Type/Class | 2D Diagram | 3D Interactions |
PRD_900117 Query on PRD_900117 | C, D | 4beta-beta-xylotriose | Oligosaccharide / Metabolism |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 1.90 Å
- R-Value Free: 0.194 
- R-Value Work: 0.164 
- R-Value Observed: 0.166 
- Space Group: P 32 2 1
Unit Cell:
Length ( Å ) | Angle ( ˚ ) |
---|---|
a = 173.178 | α = 90 |
b = 173.178 | β = 90 |
c = 131.71 | γ = 120 |
Software Name | Purpose |
---|---|
REFMAC | refinement |
MOSFLM | data reduction |
SCALA | data scaling |
SHELX | phasing |
SOLVE | phasing |
RESOLVE | phasing |
Entry History 
Deposition Data
- Released Date: 2010-01-19  Deposition Author(s): Najmudin, S., Pinheiro, B.A., Romao, M.J., Prates, J.A.M., Fontes, C.M.G.A.
Revision History (Full details and data files)
- Version 1.0: 2010-01-19
Type: Initial release - Version 1.1: 2011-07-13
Changes: Advisory, Version format compliance - Version 1.2: 2012-01-18
Changes: Other - Version 1.3: 2019-05-08
Changes: Data collection, Derived calculations, Experimental preparation, Other - Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Derived calculations, Other, Structure summary