3GHD

Crystal structure of a cystathionine beta-synthase domain protein fused to a Zn-ribbon-like domain

• PDB DOI: https://doi.org/10.2210/pdb3GHD/pdb
• Entry: 3GHD supersedes: 3FIO

• Classification: Nucleotide binding protein, Metal binding protein
• Organism(s): Pyrococcus furiosus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2009-03-03 Released: 2009-03-31 
• Deposition Author(s): Dong, A., Xu, X., Chruszcz, M., Brown, G., Proudfoot, M., Edwards, A.M., Joachimiak, A., Minor, W., Savchenko, A., Yaleunin, A., Midwest Center for Structural Genomics (MCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.81 Å
• R-Value Free: 0.241 
• R-Value Work: 0.192 
• R-Value Observed: 0.195 

Literature

Crystal structure of a cystathionine beta-synthase domain protein fused to a Zn-ribbon-like domain

Dong, A., Xu, X., Chruszcz, M., Brown, G., Proudfoot, M., Edwards, A.M., Joachimiak, A., Minor, W., Savchenko, A., Yaleunin, A.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (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 generated by PISA (software)

Biological Assembly 3  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 3 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 15.49 kDa 
• Atom Count: 1,139 
• Modelled Residue Count: 140 
• Deposited Residue Count: 140 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
a cystathionine beta-synthase domain protein fused to a Zn-ribbon-like domain	A, B	70	Pyrococcus furiosus	Mutation(s): 0
UniProt
Find proteins for Q8TZN4 (Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1)) Explore Q8TZN4  Go to UniProtKB:  Q8TZN4

Small Molecules

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: 1.81 Å
• R-Value Free: 0.241 
• R-Value Work: 0.192 
• R-Value Observed: 0.195 
• Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 54.153	α = 90
b = 73.162	β = 90
c = 35.264	γ = 90

Software Package:

Software Name	Purpose
Blu-Ice	data collection
SOLVE	phasing
RESOLVE	model building
REFMAC	refinement
Coot	model building
HKL-2000	data reduction
HKL-2000	data scaling
RESOLVE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-03-31 
Deposition Author(s): Dong, A., Xu, X., Chruszcz, M., Brown, G., Proudfoot, M., Edwards, A.M., Joachimiak, A., Minor, W., Savchenko, A., Yaleunin, A., Midwest Center for Structural Genomics (MCSG)
• This entry supersedes: 3FIO

Revision History  

• Version 1.0: 2009-03-31
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Refinement description, Version format compliance
• Version 1.2: 2012-04-04
  Changes: Structure summary
• Version 1.3: 2018-01-24
  Changes: Database references
• Version 1.4: 2022-04-13
  Changes: Database references, Derived calculations, Structure summary
• Version 1.5: 2024-11-20
  Changes: Data collection, Structure summary