5XC2

Crystal structure of GH family 81 beta-1,3-glucanase from Rhizomucr miehei complexed with laminarihexaose


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.176 
  • R-Value Observed: 0.178 

wwPDB Validation   3D Report Full Report


This is version 2.0 of the entry. See complete history


Literature

Catalytic mechanism of glycoside hydrolase family 81 beta-1,3-glucanase

Yang, S.Qin, Z.Zhou, P.Yan, Q.Jiang, Z.

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Endo-beta-1,3-glucanaseA, B, C, D796Rhizomucor mieheiMutation(s): 0 
EC: 3.2.1.39 (PDB Primary Data), 3.2.1.6 (UniProt)
UniProt
Find proteins for A0A023I7E1 (Rhizomucor miehei)
Explore A0A023I7E1 
Go to UniProtKB:  A0A023I7E1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A023I7E1
Protein Feature View
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 2
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
beta-D-glucopyranose-(1-3)-beta-D-glucopyranose-(1-3)-beta-D-glucopyranose-(1-3)-beta-D-glucopyranose-(1-3)-beta-D-glucopyranose-(1-3)-beta-D-glucopyranoseE 6N/A Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G41202OE
GlyCosmos:  G41202OE
GlyGen:  G41202OE
Entity ID: 3
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
beta-D-glucopyranose-(1-3)-beta-D-glucopyranose-(1-3)-beta-D-glucopyranose-(1-3)-beta-D-glucopyranose-(1-3)-beta-D-glucopyranoseF, M 5N/A Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G03330ED
GlyCosmos:  G03330ED
Entity ID: 4
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
beta-D-glucopyranose-(1-3)-beta-D-glucopyranose-(1-3)-beta-D-glucopyranose-(1-3)-beta-D-glucopyranoseG, L, O, P, Q 4N/A Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G87841AX
GlyCosmos:  G87841AX
GlyGen:  G87841AX
Entity ID: 5
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
beta-D-glucopyranose-(1-3)-beta-D-glucopyranose-(1-3)-beta-D-glucopyranoseH, I, N, R 3N/A Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G00024MO
GlyCosmos:  G00024MO
GlyGen:  G00024MO
Entity ID: 6
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
beta-D-glucopyranose-(1-3)-beta-D-glucopyranoseJ, K 2N/A Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G36535HU
GlyCosmos:  G36535HU
Biologically Interesting Molecules (External Reference) 1 Unique
Entity ID: 6
IDChainsNameType/Class2D Diagram3D Interactions
PRD_900024
Query on PRD_900024
J, Kbeta-laminaribioseOligosaccharide / Antimicrobial Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.176 
  • R-Value Observed: 0.178 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 108.7α = 90
b = 99.02β = 111.35
c = 138.43γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2018-03-28
    Type: Initial release
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary