3FYN | pdb_00003fyn

Crystal structure from the mobile metagenome of Cole Harbour Salt Marsh: Integron Cassette Protein HFX_CASS3

• PDB DOI: https://doi.org/10.2210/pdb3FYN/pdb

• Classification: STRUCTURAL GENOMICS, UNKNOWN FUNCTION
• Organism(s): uncultured bacterium
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2009-01-22 Released: 2009-02-10 
• Deposition Author(s): Sureshan, V., Deshpande, C.N., Harrop, S.J., Kudritska, M., Koenig, J.E., Evdokimova, E., Osipiuk, J., Edwards, A.M., Savchenko, A., Joachimiak, A., Doolittle, W.F., Stokes, H.W., Curmi, P.M.G., Mabbutt, B.C., Midwest Center for Structural Genomics (MCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.45 Å
• R-Value Free: 
  0.207 (Depositor), 0.200 (DCC) 
• R-Value Work: 
  0.179 (Depositor), 0.172 (DCC) 
• R-Value Observed: 
  0.181 (Depositor) 

Literature

Structure from the mobile metagenome of Cole Harbour Salt Marsh: Integron Cassette Protein HFX_CASS3

Sureshan, V., Deshpande, C., Harrop, S.J., Kudritska, M., Koenig, J.E., Evdokimova, E., Osipiuk, J., Edwards, A.M., Savchenko, A., Joachimiak, A., Doolittle, W.F., Stokes, H.W., Curmi, P.M.G., Mabbutt, B.C.

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)

Macromolecule Content 

• Total Structure Weight: 19.33 kDa 
• Atom Count: 1,353 
• Modeled Residue Count: 152 
• Deposited Residue Count: 176 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Integron gene cassette protein HFX_CASS3	A	176	uncultured bacterium	Mutation(s): 0  Gene Names: ORF1
UniProt
Find proteins for A0ACD6B9H1 (uncultured bacterium) Explore A0ACD6B9H1  Go to UniProtKB:  A0ACD6B9H1

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ACT	C [auth A]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M
MG	B [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-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: 1.45 Å
• R-Value Free:  0.207 (Depositor), 0.200 (DCC) 
• R-Value Work:  0.179 (Depositor), 0.172 (DCC) 
• R-Value Observed: 0.181 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.827	α = 90
b = 62.374	β = 90
c = 37.247	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-3000	data collection
HKL-3000	data reduction
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-02-10 
Deposition Author(s): Sureshan, V., Deshpande, C.N., Harrop, S.J., Kudritska, M., Koenig, J.E., Evdokimova, E., Osipiuk, J., Edwards, A.M., Savchenko, A., Joachimiak, A., Doolittle, W.F., Stokes, H.W., Curmi, P.M.G., Mabbutt, B.C., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2009-02-10
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-11-01
  Changes: Refinement description
• Version 1.3: 2024-11-06
  Changes: Data collection, Database references, Derived calculations, Structure summary