4PVI | pdb_00004pvi

Crystal structure of GH62 hydrolase in complex with xylotriose

• PDB DOI: https://doi.org/10.2210/pdb4PVI/pdb

• Classification: HYDROLASE
• Organism(s): Mycothermus thermophilus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2014-03-17 Released: 2014-09-24 
• Deposition Author(s): Nocek, B., Kaur, A.P., Xu, X., Cui, H., Savchenko, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.48 Å
• R-Value Free: 
  0.159 (Depositor), 0.171 (DCC) 
• R-Value Work: 
  0.129 (Depositor), 0.145 (DCC) 
• R-Value Observed: 
  0.130 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of GH62 hydrolase in complex with xylotriose

Kaur, A.P., Nocek, B., Xu, X., Lowden, M.J., Leyva, J.F., Stogios, P.J., Cui, H., Leo, R.D., Powlowski, J., Tsang, A., Savchenko, A.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 39.57 kDa 
• Atom Count: 3,242 
• Modeled Residue Count: 328 
• Deposited Residue Count: 342 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
GH62 hydrolase	A	342	Mycothermus thermophilus	Mutation(s): 0  EC: 3.2.1.55
UniProt
Find proteins for A0A059U759 (Humicola insolens) Explore A0A059U759  Go to UniProtKB:  A0A059U759

Oligosaccharides

Help  

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
beta-D-xylopyranose-(1-4)-beta-D-xylopyranose-(1-4)-beta-D-xylopyranose	B	3		N/A
Glycosylation Resources
GlyTouCan: G87429QT GlyCosmos: G87429QT

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PO4	C [auth A], D [auth A]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K

Biologically Interesting Molecules (External Reference) 

1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900117	B	4beta-beta-xylotriose	Oligosaccharide / Metabolism

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.48 Å
• R-Value Free:  0.159 (Depositor), 0.171 (DCC) 
• R-Value Work:  0.129 (Depositor), 0.145 (DCC) 
• R-Value Observed: 0.130 (Depositor) 

Space Group: P 3₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 72.445	α = 90
b = 72.445	β = 90
c = 62.099	γ = 120

Software Package:

Software Name	Purpose
SBC-Collect	data collection
MOLREP	phasing
CCP4	model building
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
CCP4	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-09-24 
Deposition Author(s): Nocek, B., Kaur, A.P., Xu, X., Cui, H., Savchenko, A.

Revision History  

• Version 1.0: 2014-09-24
  Type: Initial release
  
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary
• Version 2.1: 2023-09-20
  Changes: Data collection, Database references, Refinement description, Structure summary