2BDR | pdb_00002bdr

Crystal Structure of the Putative Ureidoglycolate hydrolase PP4288 from Pseudomonas putida, Northeast Structural Genomics Target PpR49

• PDB DOI: https://doi.org/10.2210/pdb2BDR/pdb

• Classification: HYDROLASE
• Organism(s): Pseudomonas putida KT2440
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2005-10-20 Released: 2005-11-15 
• Deposition Author(s): Forouhar, F., Abashidze, M., Jayaraman, S., Ho, C.K., Conover, K., Acton, T.B., Montelione, G.T., Hunt, J.F., Tong, L., Northeast Structural Genomics Consortium (NESG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 
  0.218 (Depositor), 0.225 (DCC) 
• R-Value Work: 
  0.198 (Depositor), 0.206 (DCC) 
• R-Value Observed: 
  0.198 (Depositor) 

Literature

Crystal Structure of the Putative Ureidoglycolate hydrolase PP4288 from Pseudomonas putida, Northeast Structural Genomics Target PpR49

Forouhar, F., Abashidze, M., Jayaraman, S., Ho, C.K., Conover, K., Acton, T.B., Montelione, G.T., Hunt, J.F., Tong, L.

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: 40.45 kDa 
• Atom Count: 2,958 
• Modeled Residue Count: 332 
• Deposited Residue Count: 350 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ureidoglycolate hydrolase	A, B	175	Pseudomonas putida KT2440	Mutation(s): 7  Gene Names: allA EC: 3.5.3.19 (PDB Primary Data), 4.3.2.3 (UniProt)
UniProt
Find proteins for P59285 (Pseudomonas putida (strain ATCC 47054 / DSM 6125 / CFBP 8728 / NCIMB 11950 / KT2440)) Explore P59285  Go to UniProtKB:  P59285

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NA	C [auth A], D [auth A], E [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free:  0.218 (Depositor), 0.225 (DCC) 
• R-Value Work:  0.198 (Depositor), 0.206 (DCC) 
• R-Value Observed: 0.198 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 83.027	α = 90
b = 55.268	β = 93.98
c = 81.843	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
SnB	phasing
SOLVE	phasing
RESOLVE	phasing
XTALVIEW	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-11-15 
Deposition Author(s): Forouhar, F., Abashidze, M., Jayaraman, S., Ho, C.K., Conover, K., Acton, T.B., Montelione, G.T., Hunt, J.F., Tong, L., Northeast Structural Genomics Consortium (NESG)

Revision History  

• Version 1.0: 2005-11-15
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Source and taxonomy, Version format compliance
• Version 1.3: 2017-10-18
  Changes: Refinement description
• Version 1.4: 2024-10-16
  Changes: Data collection, Database references, Derived calculations, Structure summary