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(-) Description

Title :  GFP/S205V MUTANT
 
Authors :  X. Shu, S. J. Remington
Date :  12 Jul 07  (Deposition) - 12 Feb 08  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.59
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Biol. Unit 4:  D  (1x)
Keywords :  Gfp Mutant, Alternative Excited State Proton Transfer Pathway, Fluorescent Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  X. Shu, P. Leiderman, R. Gepshtein, N. R. Smith, K. Kallio, D. Huppert, S. J. Remington
An Alternative Excited-State Proton Transfer Pathway In Green Fluorescent Protein Variant S205V.
Protein Sci. V. 16 2703 2007
PubMed-ID: 17965188  |  Reference-DOI: 10.1110/PS.073112007
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - GREEN FLUORESCENCE PROTEIN
    ChainsA, B, C, D
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    MutationYES
    Organism ScientificAZOTOBACTER VINELANDII
    Organism Taxid354

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit ABCD
Biological Unit 1 (1x)A   
Biological Unit 2 (1x) B  
Biological Unit 3 (1x)  C 
Biological Unit 4 (1x)   D

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 8)

Asymmetric Unit (2, 8)
No.NameCountTypeFull Name
1CRO4Mod. Amino Acid{2-[(1R,2R)-1-AMINO-2-HYDROXYPROPYL]-4-(4-HYDROXYBENZYLIDENE)-5-OXO-4,5-DIHYDRO-1H-IMIDAZOL-1-YL}ACETIC ACID
2IMD4Ligand/IonIMIDAZOLE
Biological Unit 1 (2, 2)
No.NameCountTypeFull Name
1CRO1Mod. Amino Acid{2-[(1R,2R)-1-AMINO-2-HYDROXYPROPYL]-4-(4-HYDROXYBENZYLIDENE)-5-OXO-4,5-DIHYDRO-1H-IMIDAZOL-1-YL}ACETIC ACID
2IMD1Ligand/IonIMIDAZOLE
Biological Unit 2 (2, 2)
No.NameCountTypeFull Name
1CRO1Mod. Amino Acid{2-[(1R,2R)-1-AMINO-2-HYDROXYPROPYL]-4-(4-HYDROXYBENZYLIDENE)-5-OXO-4,5-DIHYDRO-1H-IMIDAZOL-1-YL}ACETIC ACID
2IMD1Ligand/IonIMIDAZOLE
Biological Unit 3 (2, 2)
No.NameCountTypeFull Name
1CRO1Mod. Amino Acid{2-[(1R,2R)-1-AMINO-2-HYDROXYPROPYL]-4-(4-HYDROXYBENZYLIDENE)-5-OXO-4,5-DIHYDRO-1H-IMIDAZOL-1-YL}ACETIC ACID
2IMD1Ligand/IonIMIDAZOLE
Biological Unit 4 (2, 2)
No.NameCountTypeFull Name
1CRO1Mod. Amino Acid{2-[(1R,2R)-1-AMINO-2-HYDROXYPROPYL]-4-(4-HYDROXYBENZYLIDENE)-5-OXO-4,5-DIHYDRO-1H-IMIDAZOL-1-YL}ACETIC ACID
2IMD1Ligand/IonIMIDAZOLE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:144 , TYR A:145 , VAL A:205 , LEU A:207 , TYR C:39 , LYS C:41 , HOH C:388BINDING SITE FOR RESIDUE IMD A 239
2AC2SOFTWAREASN B:144 , TYR B:145 , VAL B:205 , LEU B:207 , HOH B:467 , TYR D:39 , LYS D:41BINDING SITE FOR RESIDUE IMD B 239
3AC3SOFTWARETYR A:39 , LYS A:41 , ASN C:144 , TYR C:145 , VAL C:205 , LEU C:207BINDING SITE FOR RESIDUE IMD C 239
4AC4SOFTWARETYR B:39 , LYS B:41 , ASN D:144 , TYR D:145 , VAL D:205 , ALA D:206 , LEU D:207BINDING SITE FOR RESIDUE IMD D 239

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2QLE)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Met A:88 -Pro A:89
2Met B:88 -Pro B:89
3Met C:88 -Pro C:89
4Met D:88 -Pro D:89

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2QLE)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2QLE)

(-) Exons   (0, 0)

(no "Exon" information available for 2QLE)

(-) Sequences/Alignments

Asymmetric Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it)
Chain A from PDB  Type:PROTEIN  Length:227
 aligned with Q8GHE2_AZOVI | Q8GHE2 from UniProtKB/TrEMBL  Length:238

    Alignment length:229
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223         
         Q8GHE2_AZOVI     4 GEELFTGVVPILVELDGDVNGHKFSVSGEGEGDATYGKLTLKFICTTGKLPVPWPTLVTTFSYGVQCFSRYPDHMKRHDFFKSAMPEGYVQERTIFFKDDGNYKTRAEVKFEGDTLVNRIELKGIDFKEDGNILGHKLEYNYNSHNVYIMADKQKNGIKVNFKIRHNIEDGSVQLADHYQQNTPIGDGPVLLPDNHYLSTQSALSKDPNEKRDHMVLLEFVTAAGITHG 232
               SCOP domains d2qlea_ A: automated matches                                                                                                                                                                                                          SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhh.eeeeeeeeeeee..eeeeeeeeeeee....eeeeeeee.......hhhhhh...--.hhhhh..hhhhhhhhhhhhh....eeeeeeeee....eeeeeeeeeee..eeeeeeeeeee...................eeeeeeee....eeeeeeeeeee.....eeeeeeeeeeee...........eeeeeeeeee........eeeeeeeeeee..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2qle A   4 GEELFTGVVPILVELDGDVNGHKFSVSGEGEGDATYGKLTLKFICTTGKLPVPWPTLVTTF--gVQCFSRYPDHMKRHDFFKSAMPEGYVQERTIFFKDDGNYKTRAEVKFEGDTLVNRIELKGIDFKEDGNILGHKLEYNYNSHNVYIMADKQKNGIKVNFKIRHNIEDGSVQLADHYQQNTPIGDGPVLLPDNHYLSTQVALSKDPNEKRDHMVLLEFVTAAGITHG 232
                                    13        23        33        43        53        63|  ||   73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223         
                                                                                       64  ||                                                                                                                                                                    
                                                                                          66-CRO                                                                                                                                                                 
                                                                                           68                                                                                                                                                                    

Chain B from PDB  Type:PROTEIN  Length:226
 aligned with Q8GHE2_AZOVI | Q8GHE2 from UniProtKB/TrEMBL  Length:238

    Alignment length:228
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223        
         Q8GHE2_AZOVI     4 GEELFTGVVPILVELDGDVNGHKFSVSGEGEGDATYGKLTLKFICTTGKLPVPWPTLVTTFSYGVQCFSRYPDHMKRHDFFKSAMPEGYVQERTIFFKDDGNYKTRAEVKFEGDTLVNRIELKGIDFKEDGNILGHKLEYNYNSHNVYIMADKQKNGIKVNFKIRHNIEDGSVQLADHYQQNTPIGDGPVLLPDNHYLSTQSALSKDPNEKRDHMVLLEFVTAAGITH 231
               SCOP domains d2qleb_ B: automated matches                                                                                                                                                                                                         SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author hhhhhh.eeeeeeeeeeee..eeeeeeeeeeee....eeeeeeee.......hhhhhh...--.hhhhh..hhhhhhhhhhhhh....eeeeeeeee....eeeeeeeeeee..eeeeeeeeeee...................eeeeeee......eeeeeeeeee.....eeeeeeeeeeee...........eeeeeeeeee........eeeeeeeeeee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2qle B   4 GEELFTGVVPILVELDGDVNGHKFSVSGEGEGDATYGKLTLKFICTTGKLPVPWPTLVTTF--gVQCFSRYPDHMKRHDFFKSAMPEGYVQERTIFFKDDGNYKTRAEVKFEGDTLVNRIELKGIDFKEDGNILGHKLEYNYNSHNVYIMADKQKNGIKVNFKIRHNIEDGSVQLADHYQQNTPIGDGPVLLPDNHYLSTQVALSKDPNEKRDHMVLLEFVTAAGITH 231
                                    13        23        33        43        53        63|  ||   73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223        
                                                                                       64  ||                                                                                                                                                                   
                                                                                          66-CRO                                                                                                                                                                
                                                                                           68                                                                                                                                                                   

Chain C from PDB  Type:PROTEIN  Length:226
 aligned with Q8GHE2_AZOVI | Q8GHE2 from UniProtKB/TrEMBL  Length:238

    Alignment length:228
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223        
         Q8GHE2_AZOVI     4 GEELFTGVVPILVELDGDVNGHKFSVSGEGEGDATYGKLTLKFICTTGKLPVPWPTLVTTFSYGVQCFSRYPDHMKRHDFFKSAMPEGYVQERTIFFKDDGNYKTRAEVKFEGDTLVNRIELKGIDFKEDGNILGHKLEYNYNSHNVYIMADKQKNGIKVNFKIRHNIEDGSVQLADHYQQNTPIGDGPVLLPDNHYLSTQSALSKDPNEKRDHMVLLEFVTAAGITH 231
               SCOP domains d2qlec_ C: automated matches                                                                                                                                                                                                         SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author hhhhhh..eeeeeeeeeee..eeeeeeeeeeee....eeeeeeee.......hhhhhh...--.hhhhh..hhhhhhhhhhhhh....eeeeeeeee....eeeeeeeeeee..eeeeeeeeeee...................eeeeeeeehhhheeeeeeeeeee.....eeeeeeeeeeee...........eeeeeeeeee........eeeeeeeeeee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2qle C   4 GEELFTGVVPILVELDGDVNGHKFSVSGEGEGDATYGKLTLKFICTTGKLPVPWPTLVTTF--gVQCFSRYPDHMKRHDFFKSAMPEGYVQERTIFFKDDGNYKTRAEVKFEGDTLVNRIELKGIDFKEDGNILGHKLEYNYNSHNVYIMADKQKNGIKVNFKIRHNIEDGSVQLADHYQQNTPIGDGPVLLPDNHYLSTQVALSKDPNEKRDHMVLLEFVTAAGITH 231
                                    13        23        33        43        53        63|  ||   73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223        
                                                                                       64  ||                                                                                                                                                                   
                                                                                          66-CRO                                                                                                                                                                
                                                                                           68                                                                                                                                                                   

Chain D from PDB  Type:PROTEIN  Length:226
 aligned with Q8GHE2_AZOVI | Q8GHE2 from UniProtKB/TrEMBL  Length:238

    Alignment length:228
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223        
         Q8GHE2_AZOVI     4 GEELFTGVVPILVELDGDVNGHKFSVSGEGEGDATYGKLTLKFICTTGKLPVPWPTLVTTFSYGVQCFSRYPDHMKRHDFFKSAMPEGYVQERTIFFKDDGNYKTRAEVKFEGDTLVNRIELKGIDFKEDGNILGHKLEYNYNSHNVYIMADKQKNGIKVNFKIRHNIEDGSVQLADHYQQNTPIGDGPVLLPDNHYLSTQSALSKDPNEKRDHMVLLEFVTAAGITH 231
               SCOP domains d2qled_ D: automated matches                                                                                                                                                                                                         SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
           Pfam domains (1) -GFP-2qleD01 D:5-229                                                                                                                                                                                                              -- Pfam domains (1)
           Pfam domains (2) -GFP-2qleD02 D:5-229                                                                                                                                                                                                              -- Pfam domains (2)
           Pfam domains (3) -GFP-2qleD03 D:5-229                                                                                                                                                                                                              -- Pfam domains (3)
           Pfam domains (4) -GFP-2qleD04 D:5-229                                                                                                                                                                                                              -- Pfam domains (4)
         Sec.struct. author hhhhhh..eeeeeeeeeee..eeeeeeeeeeee....eeeeeeee.......hhhhhh...--.hhhhh..hhhhhhhhhhhhh....eeeeeeeee....eeeeeeeeeee..eeeeeeeeeee...................eeeeeeee....eeeeeeeeeee.....eeeeeeeeeeee...........eeeeeeeeee........eeeeeeeeeee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2qle D   4 GEELFTGVVPILVELDGDVNGHKFSVSGEGEGDATYGKLTLKFICTTGKLPVPWPTLVTTF--gVQCFSRYPDHMKRHDFFKSAMPEGYVQERTIFFKDDGNYKTRAEVKFEGDTLVNRIELKGIDFKEDGNILGHKLEYNYNSHNVYIMADKQKNGIKVNFKIRHNIEDGSVQLADHYQQNTPIGDGPVLLPDNHYLSTQVALSKDPNEKRDHMVLLEFVTAAGITH 231
                                    13        23        33        43        53        63|  ||   73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223        
                                                                                       64  ||                                                                                                                                                                   
                                                                                          66-CRO                                                                                                                                                                
                                                                                           68                                                                                                                                                                   

   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (1, 4)

Asymmetric Unit

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2QLE)

(-) Pfam Domains  (1, 4)

Asymmetric Unit
(-)
Clan: GFP (101)
(-)
Family: GFP (101)
1aGFP-2qleD01D:5-229
1bGFP-2qleD02D:5-229
1cGFP-2qleD03D:5-229
1dGFP-2qleD04D:5-229

(-) Gene Ontology  (2, 2)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (Q8GHE2_AZOVI | Q8GHE2)
biological process
    GO:0008218    bioluminescence    The production of light by certain enzyme-catalyzed reactions in cells.
    GO:0006091    generation of precursor metabolites and energy    The chemical reactions and pathways resulting in the formation of precursor metabolites, substances from which energy is derived, and any process involved in the liberation of energy from these substances.

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