3FS2 | pdb_00003fs2

Crystal structure of 2-Dehydro-3-Deoxyphosphooctonate aldolase from Bruciella melitensis at 1.85A resolution

• PDB DOI: https://doi.org/10.2210/pdb3FS2/pdb

• Classification: TRANSFERASE
• Organism(s): Brucella melitensis
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2009-01-09 Released: 2009-01-20 
• Deposition Author(s): SSGCID, Seattle Structural Genomics Center for Infectious Disease (SSGCID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 
  0.222 (Depositor), 0.226 (DCC) 
• R-Value Work: 
  0.176 (Depositor), 0.182 (DCC) 
• R-Value Observed: 
  0.179 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of 2-Dehydro-3-Deoxyphosphooctonate aldolase from Bruciella melitensis at 1.85A resolution

SSGCID

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 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)

Macromolecule Content 

• Total Structure Weight: 64.48 kDa 
• Atom Count: 4,131 
• Modeled Residue Count: 507 
• Deposited Residue Count: 596 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
2-dehydro-3-deoxyphosphooctonate aldolase	A, B	298	Brucella melitensis	Mutation(s): 0  Gene Names: 3787797, BMEI0850, kdsA EC: 2.5.1.55
UniProt
Find proteins for Q8YHF1 (Brucella melitensis biotype 1 (strain ATCC 23456 / CCUG 17765 / NCTC 10094 / 16M)) Explore Q8YHF1  Go to UniProtKB:  Q8YHF1

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PG4	D [auth A], E [auth A], G [auth B]	TETRAETHYLENE GLYCOL C8 H18 O5 UWHCKJMYHZGTIT-UHFFFAOYSA-N
PO4	C [auth A], F [auth B]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free:  0.222 (Depositor), 0.226 (DCC) 
• R-Value Work:  0.176 (Depositor), 0.182 (DCC) 
• R-Value Observed: 0.179 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M33FS2

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 121.53	α = 90
b = 75.64	β = 126
c = 74.65	γ = 90

Software Package:

Software Name	Purpose
PHASER	phasing
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-01-20 
Deposition Author(s): SSGCID, Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History  

• Version 1.0: 2009-01-20
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2018-01-24
  Changes: Database references, Structure summary
• Version 1.3: 2023-09-06
  Changes: Data collection, Database references, Derived calculations, Refinement description