4WNH | pdb_00004wnh

Crystal structure of mouse Xyloside xylosyltransferase 1 complexed with manganese,acceptor ligand and UDP-Xylose

• PDB DOI: https://doi.org/10.2210/pdb4WNH/pdb

• Classification: transferase/protein binding
• Organism(s): Mus musculus, Homo sapiens
• Expression System: Homo sapiens, Escherichia coli
• Mutation(s): No 


• Deposited: 2014-10-11 Released: 2015-09-30 
• Deposition Author(s): Yu, H., Li, H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 
  0.224 (Depositor), 0.232 (DCC) 
• R-Value Work: 
  0.193 (Depositor), 0.197 (DCC) 
• R-Value Observed: 
  0.194 (Depositor) 

Literature

Crystal structure of mouse Xyloside xylosyltransferase 1 complexed with manganese,acceptor ligand and UDP-Xylose

Yu, H., Li, H.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Macromolecule Content 

• Total Structure Weight: 41.91 kDa 
• Atom Count: 2,841 
• Modeled Residue Count: 333 
• Deposited Residue Count: 356 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Xyloside xylosyltransferase 1	A	306	Mus musculus	Mutation(s): 0  Gene Names: Xxylt1 EC: 2.4.2 (PDB Primary Data), 2.4.2.62 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q3U4G3 (Mus musculus) Explore Q3U4G3  Go to UniProtKB:  Q3U4G3
IMPC:  MGI:2146443

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Coagulation factor IX	B [auth D]	50	Homo sapiens	Mutation(s): 0  Gene Names: F9 EC: 3.4.21.22
UniProt & NIH Common Fund Data Resources
Find proteins for P00740 (Homo sapiens) Explore P00740  Go to UniProtKB:  P00740
PHAROS:  P00740 GTEx:  ENSG00000101981
Glycosylation
Glycosylation Sites: 1		Go to GlyGen: P00740-1

Oligosaccharides

Help  

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
alpha-D-xylopyranose-(1-3)-beta-D-glucopyranose	C [auth B]	2		O-Glycosylation
Glycosylation Resources
GlyTouCan: G01629YL GlyCosmos: G01629YL GlyGen: G01629YL

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
UDX	E [auth A]	URIDINE-5'-DIPHOSPHATE-XYLOPYRANOSE C14 H22 N2 O16 P2 DQQDLYVHOTZLOR-OCIMBMBZSA-N
MN	D [auth A]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free:  0.224 (Depositor), 0.232 (DCC) 
• R-Value Work:  0.193 (Depositor), 0.197 (DCC) 
• R-Value Observed: 0.194 (Depositor) 

Space Group: P 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 89.481	α = 90
b = 89.481	β = 90
c = 42.895	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-09-30 
Deposition Author(s): Yu, H., Li, H.

Revision History  

• Version 1.0: 2015-09-30
  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: 2023-12-27
  Changes: Data collection, Database references, Structure summary
• Version 2.2: 2024-10-23
  Changes: Structure summary