1XRH

Crystal Structure of Ureidoglycolate Dehydrogenase from Escherichia Coli

• PDB DOI: https://doi.org/10.2210/pdb1XRH/pdb

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


• Deposited: 2004-10-14 Released: 2004-10-26 
• Deposition Author(s): Rajashankar, K.R., Kniewel, R., Lima, C.D., Burley, S.K., New York SGX Research Center for Structural Genomics (NYSGXRC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.25 Å
• R-Value Free: 0.250 
• R-Value Work: 0.192 
• R-Value Observed: 0.192 

Literature

Crystal Structure of Ureidoglycolate Dehydrogenase from Escherichia Coli

Rajashankar, K.R., Kniewel, R., Lima, C.D.

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 2  

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

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

Biological Assembly 3  

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

Biological assembly 3 assigned by authors and generated by PISA (software)

Biological Assembly 4  

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

Biological assembly 4 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 309.59 kDa 
• Atom Count: 21,480 
• Modelled Residue Count: 2,734 
• Deposited Residue Count: 2,808 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ureidoglycolate Dehydrogenase	A, B, C, D, E, F, G, H	351	Escherichia coli	Mutation(s): 12  Gene Names: ALLD EC: 1.1.1.154
UniProt
Find proteins for P77555 (Escherichia coli (strain K12)) Explore P77555  Go to UniProtKB:  P77555

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B, C, D, E, F, G, H	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.25 Å
• R-Value Free: 0.250 
• R-Value Work: 0.192 
• R-Value Observed: 0.192 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 104.715	α = 90
b = 129.916	β = 95.77
c = 106.468	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing
BEAST	model building
SHARP	phasing
RESOLVE	model building
CNS	refinement
BEAST	phasing
RESOLVE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2004-10-26 
Deposition Author(s): Rajashankar, K.R., Kniewel, R., Lima, C.D., Burley, S.K., New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History  

• Version 1.0: 2004-10-26
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2018-10-03
  Changes: Data collection, Refinement description
• Version 1.4: 2021-02-03
  Changes: Database references, Derived calculations, Structure summary
• Version 1.5: 2023-08-23
  Changes: Data collection, Database references, Refinement description
• Version 1.6: 2023-11-15
  Changes: Data collection