8QPS | pdb_00008qps

Deoxyribose-5-phosphate aldolase (DERA) from Geobacillus sp.

• PDB DOI: https://doi.org/10.2210/pdb8QPS/pdb

• Classification: LYASE
• Organism(s): Geobacillus sp.
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2023-10-03 Released: 2024-10-16 
• Deposition Author(s): Paakkonen, J., Hakulinen, N., Rouvinen, J.
• Funding Organization(s): Academy of Finland

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.64 Å
• R-Value Free: 
  0.236 (Depositor), 0.236 (DCC) 
• R-Value Work: 
  0.192 (Depositor), 0.191 (DCC) 
• R-Value Observed: 
  0.194 (Depositor) 

Starting Model: experimental

Literature

Three-dimensional structure of deoxyribose phosphate aldolase (DERA) from thermophilic Geobacillus sp.

Paakkonen, J., Andberg, M., Voutilainen, S., Koivula, A., Hakulinen, N., Janis, J., Rouvinen, J.

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 (software)

Biological Assembly Evidence: mass spectrometry

Macromolecule Content 

• Total Structure Weight: 48.53 kDa 
• Atom Count: 3,578 
• Modeled Residue Count: 440 
• Deposited Residue Count: 460 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Deoxyribose-phosphate aldolase	A, B	230	Geobacillus sp.	Mutation(s): 0  Gene Names: deoC EC: 4.1.2.4
UniProt
Find proteins for Q5KX02 (Geobacillus kaustophilus (strain HTA426)) Explore Q5KX02  Go to UniProtKB:  Q5KX02

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.64 Å
• R-Value Free:  0.236 (Depositor), 0.236 (DCC) 
• R-Value Work:  0.192 (Depositor), 0.191 (DCC) 
• R-Value Observed: 0.194 (Depositor) 

Space Group: P 3₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.23	α = 90
b = 57.23	β = 90
c = 97.03	γ = 120

Software Package:

Software Name	Purpose
GDA	data collection
xia2	data reduction
DIALS	data reduction
XDS	data reduction
XSCALE	data scaling
Aimless	data scaling
pointless	data scaling
PHASER	phasing
PHENIX	refinement

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-10-16 
Deposition Author(s): Paakkonen, J., Hakulinen, N., Rouvinen, J.

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Funding Organization	Location	Grant Number
Academy of Finland	Finland	288677
Academy of Finland	Finland	287241
Academy of Finland	Finland	321514
Academy of Finland	Finland	321503

Revision History  

• Version 1.0: 2024-10-16
  Type: Initial release