3QZ6 | pdb_00003qz6

The crystal structure of HpcH/HpaI aldolase from Desulfitobacterium hafniense DCB-2

• PDB DOI: https://doi.org/10.2210/pdb3QZ6/pdb

• Classification: LYASE
• Organism(s): Desulfitobacterium hafniense DCB-2
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2011-03-04 Released: 2011-03-16 
• Deposition Author(s): Tan, K., Chhor, G., Clancy, S., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.172 (Depositor), 0.173 (DCC) 
• R-Value Work: 
  0.152 (Depositor), 0.154 (DCC) 
• R-Value Observed: 
  0.153 (Depositor) 

Literature

The crystal structure of HpcH/HpaI aldolase from Desulfitobacterium hafniense DCB-2

Tan, K., Chhor, G., Clancy, S., Joachimiak, A.

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 - C3  (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3 

Biological assembly 2 generated by PISA (software)

Biological Assembly 3  

Global Symmetry: Dihedral - D3  (Explore in 3D)
Global Stoichiometry: Homo 6-mer - A6 

Biological assembly 3 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 29.16 kDa 
• Atom Count: 2,253 
• Modeled Residue Count: 259 
• Deposited Residue Count: 261 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HpcH/HpaI aldolase	A	261	Desulfitobacterium hafniense DCB-2	Mutation(s): 0  Gene Names: Dhaf_2073
UniProt
Find proteins for B8FRX2 (Desulfitobacterium hafniense (strain DSM 10664 / DCB-2)) Explore B8FRX2  Go to UniProtKB:  B8FRX2

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	B [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.172 (Depositor), 0.173 (DCC) 
• R-Value Work:  0.152 (Depositor), 0.154 (DCC) 
• R-Value Observed: 0.153 (Depositor) 

Space Group: H 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 131.531	α = 90
b = 131.531	β = 90
c = 176.356	γ = 120

Software Package:

Software Name	Purpose
SBC-Collect	data collection
SHELXD	phasing
MLPHARE	phasing
DM	model building
ARP	model building
WARP	model building
HKL-3000	phasing
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
DM	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-03-16 
Deposition Author(s): Tan, K., Chhor, G., Clancy, S., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2011-03-16
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2024-10-30
  Changes: Data collection, Database references, Derived calculations, Structure summary