2C4M | pdb_00002c4m

Starch phosphorylase: structural studies explain oxyanion-dependent kinetic stability and regulatory control.

• PDB DOI: https://doi.org/10.2210/pdb2C4M/pdb

• Classification: TRANSFERASE
• Organism(s): Corynebacterium callunae
• Expression System: Escherichia coli DH5[alpha]
• Mutation(s): Yes 


• Deposited: 2005-10-20 Released: 2007-02-27 
• Deposition Author(s): Purvis, A., Nidetzky, B., Watson, K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.232 (Depositor), 0.220 (DCC) 
• R-Value Work: 
  0.216 (Depositor), 0.200 (DCC) 
• R-Value Observed: 
  0.216 (Depositor) 

Starting Model: experimental

Literature

Starch Phosphorylase: Structural Studies Explain Oxyanion-Dependent Kinetic Stability and Regulatory Control

Purvis, A., Nidetzky, B., Watson, K.

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 PQS (software)

Biological Assembly 2  

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

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

Macromolecule Content 

• Total Structure Weight: 365.56 kDa 
• Atom Count: 26,654 
• Modeled Residue Count: 3,158 
• Deposited Residue Count: 3,184 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
GLYCOGEN PHOSPHORYLASE	A, B, C, D	796	Corynebacterium callunae	Mutation(s): 1  EC: 2.4.1.1
UniProt
Find proteins for Q8KQ56 (Corynebacterium callunae) Explore Q8KQ56  Go to UniProtKB:  Q8KQ56

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PLP	E [auth A], HA [auth D], P [auth B], Y [auth C]	PYRIDOXAL-5'-PHOSPHATE C8 H10 N O6 P NGVDGCNFYWLIFO-UHFFFAOYSA-N
PO4	AA [auth C], BA [auth C], F [auth A], IA [auth D], Q [auth B], R [auth B], S [auth B], T [auth B], Z [auth C]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
EDO	GA [auth C], W [auth B], X [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
FMT	CA [auth C], DA [auth C], EA [auth C], FA [auth C], G [auth A], H [auth A], I [auth A], J [auth A], JA [auth D], K [auth A], KA [auth D], L [auth A], LA [auth D], M [auth A], MA [auth D], N [auth A], O [auth A], U [auth B], V [auth B]	FORMIC ACID C H2 O2 BDAGIHXWWSANSR-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free:  0.232 (Depositor), 0.220 (DCC) 
• R-Value Work:  0.216 (Depositor), 0.200 (DCC) 
• R-Value Observed: 0.216 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 99.266	α = 90
b = 187.62	β = 112.48
c = 129.315	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
MOSFLM	data reduction
SCALA	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-02-27 
Deposition Author(s): Purvis, A., Nidetzky, B., Watson, K.

Revision History  

• Version 1.0: 2007-02-27
  Type: Initial release
  
• Version 1.1: 2011-05-08
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2018-02-28
  Changes: Advisory, Source and taxonomy
• Version 1.4: 2019-05-08
  Changes: Data collection, Derived calculations, Experimental preparation
• Version 1.5: 2023-12-13
  Changes: Advisory, Data collection, Database references, Other, Refinement description