2ASV | pdb_00002asv

X-Ray studies on protein complexes: Enzymatic catalysis in Crystals of E. coli Maltodextrin Phosphorylase (MalP)

• PDB DOI: https://doi.org/10.2210/pdb2ASV/pdb

• Classification: TRANSFERASE
• Organism(s): Escherichia coli
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2005-08-24 Released: 2005-09-06 
• Deposition Author(s): Geremia, S., Campagnolo, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 
  0.226 (Depositor), 0.187 (DCC) 
• R-Value Work: 
  0.179 (Depositor), 0.191 (DCC) 
• R-Value Observed: 
  0.182 (Depositor) 

Starting Model: experimental

Literature

X-Ray studies on protein complexes: Enzymatic catalysis in Crystals of E.coli Maltodextrin Phosphorylase (MalP)

Geremia, S., Campagnolo, M.

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)

Macromolecule Content 

• Total Structure Weight: 183.76 kDa 
• Atom Count: 14,136 
• Modeled Residue Count: 1,592 
• Deposited Residue Count: 1,592 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Maltodextrin phosphorylase	A, B	796	Escherichia coli	Mutation(s): 3  Gene Names: EG10560 EC: 2.4.1.1
UniProt
Find proteins for P00490 (Escherichia coli (strain K12)) Explore P00490  Go to UniProtKB:  P00490

Oligosaccharides

Help  

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-beta-D-glucopyranose	C, D	5		N/A
Glycosylation Resources
GlyTouCan: G43441FW GlyCosmos: G43441FW

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PLP	G [auth A], J [auth B]	PYRIDOXAL-5'-PHOSPHATE C8 H10 N O6 P NGVDGCNFYWLIFO-UHFFFAOYSA-N
ASO	E [auth A], H [auth B]	1,5-anhydro-D-glucitol C6 H12 O5 MPCAJMNYNOGXPB-SLPGGIOYSA-N
PO4	F [auth A], I [auth B]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free:  0.226 (Depositor), 0.187 (DCC) 
• R-Value Work:  0.179 (Depositor), 0.191 (DCC) 
• R-Value Observed: 0.182 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 74.327	α = 90
b = 104.723	β = 90
c = 214.787	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MAR345	data collection
CCP4	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-09-06 
Deposition Author(s): Geremia, S., Campagnolo, M.

Revision History  

• Version 1.0: 2005-09-06
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Non-polymer description, Version format compliance
• Version 1.3: 2017-10-11
  Changes: Refinement description
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Structure summary
• Version 2.1: 2021-11-10
  Changes: Database references, Structure summary
• Version 2.2: 2023-10-25
  Changes: Data collection, Refinement description