8QME

Structural characterization of beta-xyloxidase XynB2 from Geobacillus stearothermophilus CECT43


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.178 
  • R-Value Observed: 0.179 

Starting Model: in silico
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wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Structural Characterization of beta-Xylosidase XynB2 from Geobacillus stearothermophilus CECT43: A Member of the Glycoside Hydrolase Family GH52

Gavira, J.A.Contreras, L.M.Alshamaa, H.M.Clemente-Jimenez, J.M.Rodriguez-Vico, F.Las Heras-Vazquez, F.J.Martinez-Rodriguez, S.

(2024) Crystals (Basel) 14


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Beta-xylosidase
A, B, C, D
711Geobacillus stearothermophilusMutation(s): 3 
Gene Names: GA8_03270
UniProt
Find proteins for A0A7U9HVH2 (Geobacillus sp. A8)
Explore A0A7U9HVH2 
Go to UniProtKB:  A0A7U9HVH2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A7U9HVH2
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download Ideal Coordinates CCD File 
AA [auth D]
EA [auth D]
FA [auth D]
GA [auth D]
H [auth A]
AA [auth D],
EA [auth D],
FA [auth D],
GA [auth D],
H [auth A],
HA [auth D],
I [auth A],
IA [auth D],
J [auth A],
K [auth A],
Q [auth B],
R [auth B],
S [auth B],
Y [auth C],
Z [auth C]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
GOL
Query on GOL

Download Ideal Coordinates CCD File 
BA [auth D]
DA [auth D]
E [auth A]
F [auth A]
G [auth A]
BA [auth D],
DA [auth D],
E [auth A],
F [auth A],
G [auth A],
M [auth B],
N [auth B],
P [auth B],
T [auth C],
U [auth C],
V [auth C]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
ACT
Query on ACT

Download Ideal Coordinates CCD File 
CA [auth D],
L [auth A],
O [auth B],
W [auth C],
X [auth C]
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.178 
  • R-Value Observed: 0.179 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 81.121α = 107.45
b = 97.514β = 98.48
c = 107.4γ = 106.55
Software Package:
Software NamePurpose
PHENIXrefinement
Aimlessdata scaling
MOLREPphasing
XDSdata reduction

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Ministerio de Ciencia e Innovacion (MCIN)SpainPID2020-116261GB-I00

Revision History  (Full details and data files)

  • Version 1.0: 2024-03-27
    Type: Initial release