HOMEWORK#5

Protein Data Bank

• due on 4/25

• 1. Please find the 1.9 Å crystal structure of the Aequorea victoria green fluorescent protein (GFP) from PDB. Give the following informations:
• a.) PDB ID number.
• b.) Name of the authors.
• c.) Expression system used by authors.
• d.) Residue number.
• e.) Number of helix.
• f.) The starting residue and ending residue of each helix.
• g.) Number of b-sheet.
 
• 2. Show three different Rasmol pictures of GFP:
• whatever you like.
• highlight the chromophore by spacefill and green.
• a rotating molecule by GIF builder.

• 3. A blue emission variant of GFP has been made by mutation of two residues. Please find the structure of this blue emission variant. Show its structure and color the two mutated positions blue.

• 1

 

PDB ID	1EMA	1GFL
Authers	M.Ormo, A.B.Cubitt, K.Kallio, L.A.Gross, R.Y.Tsien, S.J.Remington	F.Yang, L.G.Moss, G.N.Phillips Junior
Compound	Molecule: Green Fluorescent Protein  Chain: Null  Engineered: Yes  Mutation: 65 - 67 Replaced By Cro, Q80r  Other_details: The Protein Contains Six  Se-Methionines. Of These, The N-Terminal Met  And Met 233 Are Not Present In The Entry	Molecule: Green Fluorescent Protein  Chain: A, B  Engineered: Yes  Mutation: Q80r
Expression system	Organism_scientific: Aequorea Victoria  Organism_common: Jellyfish  Plasmid: Prsetb (Invitrogen)  Expression_system:Escherichia  Coli  Expression_system_strain: Jm109 (De3)  Other_details: The N-Terminal His-Tag Has Been Removed	Organism_scientific: Aequorea Victoria                                    Expression_system: Escherichia Coli                                    Expression_system_plasmid: Ptu58
Residue numbers	708	A chain:714 ;B chain:714
NO. of heliex	4	A chain:6 ; B chain:6
NO.of sheet	11	A chain:12 ; B chain:12
The starting residue and ending residue of each helix.	HELIX 1: GLY 4- PHE 8  HELIX 2: TRP 57 - LEU 60  HELIX 3: GLN 69 - PHE 71  HELIX 4: PHE 83 - SER 86	A chain:  HELIX1:GLU 5-PHE 8  HELIX2:TRP 57 - PHE 64  HELIX3:GLN 69 - PHE71  HELIX 4:ASP 76 - HIS 81  HELIX 5:PHE 83-SER86  HELIX6:LYS156-LYS158  B chain:  HELIX7:GLU5-PHE8  HELIX8:TRP57-PHE64  HELIX9:GLN69- PHE71  HELIX10:ASP76-HIS81  HELIX11: PHE83-SER86  HELIX12: LYS156-LYS158

 

• 2
a)
 
 
   

b)


 
 

c)


3.Mutation: S65, H66, And G67 Are  Replaced With Iic 66, Y145f


 

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PC Lyu