9WVU | pdb_00009wvu

Carbohydrate-bound structure of alpha-glucan phosphorylase from Crocosphaera subtropica ATCC 51142

• PDB DOI: https://doi.org/10.2210/pdb9WVU/pdb

• Classification: TRANSFERASE
• Organism(s): Crocosphaera subtropica ATCC 51142
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2025-09-22 Released: 2026-03-18 
• Deposition Author(s): Suzuki, R., Ikuta, A., Suzuki, E.
• Funding Organization(s): Japan Society for the Promotion of Science (JSPS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 
  0.227 (Depositor), 0.228 (DCC) 
• R-Value Work: 
  0.174 (Depositor), 0.180 (DCC) 

Starting Model: in silico

Literature

Carbohydrate-bound structure suggests a reaction model for alpha-glucan phosphorylase

Suzuki, R., Ikuta, A., Suzuki, E.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 201.56 kDa 
• Atom Count: 13,591 
• Modeled Residue Count: 1,626 
• Deposited Residue Count: 1,710 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Alpha-1,4 glucan phosphorylase	A [auth AAA], B [auth BBB]	855	Crocosphaera subtropica ATCC 51142	Mutation(s): 0  Gene Names: glgP3, cce_1603 EC: 2.4.1.1
UniProt
Find proteins for B1WXW6 (Crocosphaera subtropica (strain ATCC 51142 / BH68)) Explore B1WXW6  Go to UniProtKB:  B1WXW6

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose	C [auth CCC]	6		N/A
Glycosylation Resources
GlyTouCan:  G91368RN GlyCosmos:  G91368RN GlyGen:  G91368RN

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose	D [auth CfC]	11		N/A
Glycosylation Resources
GlyTouCan:  G30216KF GlyCosmos:  G30216KF GlyGen:  G30216KF

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose	E [auth CqC], G [auth CxC]	3		N/A
Glycosylation Resources
GlyTouCan:  G96370VA GlyCosmos:  G96370VA GlyGen:  G96370VA

Entity ID: 5
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose	F [auth CtC]	4		N/A
Glycosylation Resources
GlyTouCan:  G87171PZ GlyCosmos:  G87171PZ GlyGen:  G87171PZ

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
LLP	A [auth AAA], B [auth BBB]	L-PEPTIDE LINKING	C14 H22 N3 O7 P		LYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free:  0.227 (Depositor), 0.228 (DCC) 
• R-Value Work:  0.174 (Depositor), 0.180 (DCC) 

Diffraction Data: https://doi.org/10.18430/M39WVU

Space Group: H 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 267.238	α = 90
b = 267.238	β = 90
c = 204.452	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
iMOSFLM	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2026-03-18 
Deposition Author(s): Suzuki, R., Ikuta, A., Suzuki, E.

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Funding Organization	Location	Grant Number
Japan Society for the Promotion of Science (JSPS)	Japan	23K05682

Revision History  

• Version 1.0: 2026-03-18
  Type: Initial release