3R2E | pdb_00003r2e

Dihydroneopterin aldolase/dihydroneopterin triphosphate 2'-epimerase from Yersinia pestis.

• PDB DOI: https://doi.org/10.2210/pdb3R2E/pdb

• Classification: LYASE
• Organism(s): Yersinia pestis
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2011-03-14 Released: 2011-03-23 
• Deposition Author(s): Osipiuk, J., Maltseva, N., Makowska-Grzyska, M., Papazisi, L., Anderson, W.F., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.15 Å
• R-Value Free: 
  0.255 (Depositor), 0.260 (DCC) 
• R-Value Work: 
  0.215 (Depositor), 0.220 (DCC) 
• R-Value Observed: 
  0.217 (Depositor) 

Starting Model: experimental

Literature

Dihydroneopterin aldolase/dihydroneopterin triphosphate 2'-epimerase from Yersinia pestis

Osipiuk, J., Maltseva, N., Makowska-Grzyska, M., Papazisi, L., Anderson, W.F., Joachimiak, A.

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D4  (Explore in 3D)
Global Stoichiometry: Homo 8-mer - A8 

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

Macromolecule Content 

• Total Structure Weight: 16.15 kDa 
• Atom Count: 939 
• Modeled Residue Count: 117 
• Deposited Residue Count: 143 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dihydroneopterin aldolase	A	143	Yersinia pestis	Mutation(s): 0  Gene Names: folB, YPO0648 EC: 4.1.2.25
UniProt
Find proteins for A0A5P8YJX5 (Yersinia pestis) Explore A0A5P8YJX5  Go to UniProtKB:  A0A5P8YJX5

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.15 Å
• R-Value Free:  0.255 (Depositor), 0.260 (DCC) 
• R-Value Work:  0.215 (Depositor), 0.220 (DCC) 
• R-Value Observed: 0.217 (Depositor) 

Diffraction Data: https://doi.org/10.18430/m33r2e

Space Group: I 4 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 71.716	α = 90
b = 71.716	β = 90
c = 107.629	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
SBC-Collect	data collection
HKL-3000	data reduction
HKL-3000	data scaling
MOLREP	phasing
HKL-3000	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-03-23 
Deposition Author(s): Osipiuk, J., Maltseva, N., Makowska-Grzyska, M., Papazisi, L., Anderson, W.F., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History  

• Version 1.0: 2011-03-23
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-11-08
  Changes: Refinement description
• Version 1.3: 2023-09-13
  Changes: Data collection, Database references, Refinement description