4NDZ | pdb_00004ndz

Structure of Maltose Binding Protein fusion to 2-O-Sulfotransferase with bound heptasaccharide and PAP

• PDB DOI: https://doi.org/10.2210/pdb4NDZ/pdb

• Classification: TRANSPORT PROTEIN/TRANSFERASE
• Organism(s): Escherichia coli UMEA 3304-1, Gallus gallus
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2013-10-28 Released: 2014-03-19 
• Deposition Author(s): Liu, C., Sheng, J., Krahn, J.M., Perera, L., Xu, Y., Hsieh, P., Liu, J., Pedersen, L.C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.45 Å
• R-Value Free: 
  0.228 (Depositor), 0.230 (DCC) 
• R-Value Work: 
  0.176 (Depositor), 0.180 (DCC) 
• R-Value Observed: 
  0.177 (Depositor) 

Starting Model: experimental

Literature

Deciphering the role of 2-O-sulfotransferase in regulating heparan sulfate biosynthesis

Liu, C., Sheng, J., Krahn, J.M., Perera, L., Xu, Y., Hsieh, P., Liu, J., Pedersen, L.C.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A2B1 

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

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 3-mer - A3 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 458.29 kDa 
• Atom Count: 28,764 
• Modeled Residue Count: 3,558 
• Deposited Residue Count: 3,948 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Maltose-binding periplasmic protein, Heparan sulfate 2-O-sulfotransferase 1 fusion	A, B, C, D, E, F	658	Escherichia coli UMEA 3304-1, Gallus gallus This entity is chimeric	Mutation(s): 4  Gene Names: G962_03763, HS2ST1, HS2ST EC: 2.8.2
UniProt
Find proteins for P0AEX9 (Escherichia coli (strain K12)) Explore P0AEX9  Go to UniProtKB:  P0AEX9
Find proteins for Q76KB1 (Gallus gallus) Explore Q76KB1  Go to UniProtKB:  Q76KB1
UniProt Groups	P0AEX9Q76KB1

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-glucopyranuronic acid-(1-4)-2-acetamido-2-deoxy-alpha-D-glucopyranose-(1-4)-beta-D-glucopyranuronic acid-(1-4)-2-deoxy-2-(sulfoamino)-alpha-D-glucopyranose-(1-4)-alpha-L-idopyranuronic acid-(1-4)-2-deoxy-2-(sulfoamino)-alpha-D-glucopyranose-(1-4)-beta-D-glucopyranuronic acid	G, I, L, N, P	7		N/A
Glycosylation Resources
GlyTouCan:  G54413LX GlyCosmos:  G54413LX

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose	H, J, K, M, O	2		N/A
Glycosylation Resources
GlyTouCan:  G07411ON GlyCosmos:  G07411ON

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A3P	Q [auth A], S [auth B], U [auth C], V [auth D], X [auth E], Z [auth F]	ADENOSINE-3'-5'-DIPHOSPHATE C10 H15 N5 O10 P2 WHTCPDAXWFLDIH-KQYNXXCUSA-N
NPO	R [auth A], T [auth B], W [auth D], Y [auth E]	P-NITROPHENOL C6 H5 N O3 BTJIUGUIPKRLHP-UHFFFAOYSA-N

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 3
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900001	H, J, K, M, O	alpha-maltose	Oligosaccharide / Nutrient

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.45 Å
• R-Value Free:  0.228 (Depositor), 0.230 (DCC) 
• R-Value Work:  0.176 (Depositor), 0.180 (DCC) 
• R-Value Observed: 0.177 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 155.72	α = 90
b = 170.69	β = 90
c = 183.96	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-03-19 
Deposition Author(s): Liu, C., Sheng, J., Krahn, J.M., Perera, L., Xu, Y., Hsieh, P., Liu, J., Pedersen, L.C.

Revision History  

• Version 1.0: 2014-03-19
  Type: Initial release
  
• Version 1.1: 2017-08-16
  Changes: Refinement description, Source and taxonomy
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Structure summary
• Version 2.1: 2023-09-20
  Changes: Data collection, Database references, Refinement description, Structure summary
• Version 2.2: 2024-10-16
  Changes: Structure summary