4LYQ

Crystal Structure of Glycoside Hydrolase Family 5 Mannosidase from Rhizomucor miehei, E202A mutant

• PDB DOI: https://doi.org/10.2210/pdb4LYQ/pdb

• Classification: HYDROLASE
• Organism(s): Rhizomucor miehei
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2013-07-31 Released: 2014-08-06 
• Deposition Author(s): Jiang, Z.Q., Zhou, P., Yang, S.Q., Liu, Y., Yan, Q.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.163 
• R-Value Work: 0.125 
• R-Value Observed: 0.127 

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: 52.23 kDa 
• Atom Count: 3,849 
• Modelled Residue Count: 414 
• Deposited Residue Count: 449 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Exo-beta-1,4-mannosidase	A	449	Rhizomucor miehei	Mutation(s): 0  EC: 3.2.1.25

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-mannopyranose-(1-4)-beta-D-mannopyranose-(1-4)-alpha-D-mannopyranose	B	3		N/A
Glycosylation Resources
GlyTouCan:  G98033RN GlyCosmos:  G98033RN GlyGen:  G98033RN

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EPE	E [auth A]	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID C8 H18 N2 O4 S JKMHFZQWWAIEOD-UHFFFAOYSA-N
TRS	C [auth A], D [auth A]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C4 H12 N O3 LENZDBCJOHFCAS-UHFFFAOYSA-O

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.163 
• R-Value Work: 0.125 
• R-Value Observed: 0.127 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 131.173	α = 90
b = 76.549	β = 113.36
c = 54.836	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
PHENIX	model building
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-08-06 
Deposition Author(s): Jiang, Z.Q., Zhou, P., Yang, S.Q., Liu, Y., Yan, Q.J.

Revision History  

• Version 1.0: 2014-08-06
  Type: Initial release
  
• Version 1.1: 2014-11-26
  Changes: Database references
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary
• Version 2.1: 2023-11-08
  Changes: Data collection, Database references, Refinement description, Structure summary