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(-) Description

Title :  PADRON ON (FLUORESCENT) ABCIS
 
Authors :  A. Regis Faro, P. Carpentier, D. Bourgeois
Date :  19 Jul 11  (Deposition) - 10 Aug 11  (Release) - 09 Nov 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.34
Chains :  Asym. Unit :  A,B,C,D,E,F
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Biol. Unit 4:  D  (1x)
Biol. Unit 5:  E  (1x)
Biol. Unit 6:  F  (1x)
Keywords :  Gfp Variants, Fluorescent Protein, Positive Photoswitching, Fps, Rsfps, Cryo-Probe, Intermediate State, Isomerization (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Regis Faro, P. Carpentier, G. Jonasson, G. Pompidor, D. Arcizet, I. Demachy, D. Bourgeois
Low-Temperature Chromophore Isomerization Reveals The Photoswitching Mechanism Of The Fluorescent Protein Padron.
J. Am. Chem. Soc. V. 133 16362 2011
PubMed-ID: 21923132  |  Reference-DOI: 10.1021/JA207001Y

(-) Compounds

Molecule 1 - FLUORESCENT PROTEIN DRONPA
    Chains: A, B, C, D, E, F
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Expression System Vector: PRSET
    Expression System Vector Type: PLASMID
    Fragment: RESIDUES 2-217
    Organism Scientific: ECHINOPHYLLIA SP. SC22
    Organism Taxid: 301887
    Synonym: PADRON

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit : ABCDEF
Biological Unit 1 (1x): A     
Biological Unit 2 (1x):  B    
Biological Unit 3 (1x):   C   
Biological Unit 4 (1x):    D  
Biological Unit 5 (1x):     E 
Biological Unit 6 (1x):      F

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 6)

Asymmetric Unit (1, 6)
No.NameCountTypeFull Name
1GYC6Mod. Amino Acid[(4Z)-2-[(1R)-1-AMINO-2-MERCAPTOETHYL]-4-(4-HYDROXYBENZYLIDENE)-5-OXO-4,5-DIHYDRO-1H-IMIDAZOL-1-YL]ACETIC ACID
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1GYC1Mod. Amino Acid[(4Z)-2-[(1R)-1-AMINO-2-MERCAPTOETHYL]-4-(4-HYDROXYBENZYLIDENE)-5-OXO-4,5-DIHYDRO-1H-IMIDAZOL-1-YL]ACETIC ACID
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1GYC1Mod. Amino Acid[(4Z)-2-[(1R)-1-AMINO-2-MERCAPTOETHYL]-4-(4-HYDROXYBENZYLIDENE)-5-OXO-4,5-DIHYDRO-1H-IMIDAZOL-1-YL]ACETIC ACID
Biological Unit 3 (1, 1)
No.NameCountTypeFull Name
1GYC1Mod. Amino Acid[(4Z)-2-[(1R)-1-AMINO-2-MERCAPTOETHYL]-4-(4-HYDROXYBENZYLIDENE)-5-OXO-4,5-DIHYDRO-1H-IMIDAZOL-1-YL]ACETIC ACID
Biological Unit 4 (1, 1)
No.NameCountTypeFull Name
1GYC1Mod. Amino Acid[(4Z)-2-[(1R)-1-AMINO-2-MERCAPTOETHYL]-4-(4-HYDROXYBENZYLIDENE)-5-OXO-4,5-DIHYDRO-1H-IMIDAZOL-1-YL]ACETIC ACID
Biological Unit 5 (1, 1)
No.NameCountTypeFull Name
1GYC1Mod. Amino Acid[(4Z)-2-[(1R)-1-AMINO-2-MERCAPTOETHYL]-4-(4-HYDROXYBENZYLIDENE)-5-OXO-4,5-DIHYDRO-1H-IMIDAZOL-1-YL]ACETIC ACID
Biological Unit 6 (1, 1)
No.NameCountTypeFull Name
1GYC1Mod. Amino Acid[(4Z)-2-[(1R)-1-AMINO-2-MERCAPTOETHYL]-4-(4-HYDROXYBENZYLIDENE)-5-OXO-4,5-DIHYDRO-1H-IMIDAZOL-1-YL]ACETIC ACID

(-) Sites  (0, 0)

(no "Site" information available for 3ZUJ)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3ZUJ)

(-) Cis Peptide Bonds  (13, 13)

Asymmetric Unit
No.Residues
1Gly A:48 -Pro A:49
2Phe A:83 -Pro A:84
3Gly B:48 -Pro B:49
4Phe B:83 -Pro B:84
5Gly C:48 -Pro C:49
6Phe C:83 -Pro C:84
7Gly D:48 -Pro D:49
8Phe D:83 -Pro D:84
9Ile E:4 -Lys E:5
10Gly E:48 -Pro E:49
11Phe E:83 -Pro E:84
12Gly F:48 -Pro F:49
13Phe F:83 -Pro F:84

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3ZUJ)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3ZUJ)

(-) Exons   (0, 0)

(no "Exon" information available for 3ZUJ)

(-) 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:214
 aligned with Q5TLG6_9CNID | Q5TLG6 from UniProtKB/TrEMBL  Length:224

    Alignment length:216
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211      
         Q5TLG6_9CNID     2 SVIKPDMKIKLRMEGAVNGHPFAIEGVGLGKPFEGKQSMDLKVKEGGPLPFAYDILTTVFCYGNRVFAKYPENIVDYFKQSFPEGYSWERSMNYEDGGICNATNDITLDGDCYIYEIRFDGVNFPANGPVMQKRTVKWEPSTEKLYVRDGVLKGDVNMALSLEGGGHYRCDFKTTYKAKKVVQLPDYHFVDHHIEIKSHDKDYSNVNLHEHAEAHS 217
               SCOP domains d3zuja_ A: automated matches                                                                                                                                                                                             SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ......eeeeeeeeeee..eeeeeeeeeeee....eeeeeeeeee......hhhhh.....--............hhhhhh....eeeeeeeee....eeeeeeeeeee..eeeeeeeeeee............eeee..eeeeeeee..eeeeeeeeeeee....eeeeeeeeeeee.........eeeeeeeeeeee.....eeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3zuj A   2 SVIKPDMKIKLRMEGAVNGHPFAIEGVGLGKPFEGKQSMDLKVKEGGPLPFAYDILTMAFc--NRVFAKYPENIVDYFKQSFPEGYSWERSMIYEDGGICNATNDITLDGDCYIYEIRFDGVNFPANGPVMQKRTVKWELSTEKLYVRDGVLKSDGNYALSLEGGGHYRCDFKTTYKAKKVVQLPDYHSVDHHIEIKSHDKDYSNVNLHEHAEAHS 217
                                    11        21        31        41        51        61|  |    71        81        91       101       111       121       131       141       151       161       171       181       191       201       211      
                                                                                      61| 65                                                                                                                                                        
                                                                                       63-GYC                                                                                                                                                       


Chain B from PDB  Type:PROTEIN  Length:214
 aligned with Q5TLG6_9CNID | Q5TLG6 from UniProtKB/TrEMBL  Length:224

    Alignment length:216
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211      
         Q5TLG6_9CNID     2 SVIKPDMKIKLRMEGAVNGHPFAIEGVGLGKPFEGKQSMDLKVKEGGPLPFAYDILTTVFCYGNRVFAKYPENIVDYFKQSFPEGYSWERSMNYEDGGICNATNDITLDGDCYIYEIRFDGVNFPANGPVMQKRTVKWEPSTEKLYVRDGVLKGDVNMALSLEGGGHYRCDFKTTYKAKKVVQLPDYHFVDHHIEIKSHDKDYSNVNLHEHAEAHS 217
               SCOP domains d3zujb_ B: automated matches                                                                                                                                                                                             SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ......eeeeeeeeeee..eeeeeeeeeeee....eeeeeeeeee......hhhhh.....--..............hhhhh...eeeeeeeee....eeeeeeeeeee..eeeeeeeeeee............eeee..eeeeeeee..eeeeeeeeeeee....eeeeeeeeeeee.........eeeeeeeeeeee.....eeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3zuj B   2 SVIKPDMKIKLRMEGAVNGHPFAIEGVGLGKPFEGKQSMDLKVKEGGPLPFAYDILTMAFc--NRVFAKYPENIVDYFKQSFPEGYSWERSMIYEDGGICNATNDITLDGDCYIYEIRFDGVNFPANGPVMQKRTVKWELSTEKLYVRDGVLKSDGNYALSLEGGGHYRCDFKTTYKAKKVVQLPDYHSVDHHIEIKSHDKDYSNVNLHEHAEAHS 217
                                    11        21        31        41        51        61|  |    71        81        91       101       111       121       131       141       151       161       171       181       191       201       211      
                                                                                      61| 65                                                                                                                                                        
                                                                                       63-GYC                                                                                                                                                       


Chain C from PDB  Type:PROTEIN  Length:213
 aligned with Q5TLG6_9CNID | Q5TLG6 from UniProtKB/TrEMBL  Length:224

    Alignment length:215
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212     
         Q5TLG6_9CNID     3 VIKPDMKIKLRMEGAVNGHPFAIEGVGLGKPFEGKQSMDLKVKEGGPLPFAYDILTTVFCYGNRVFAKYPENIVDYFKQSFPEGYSWERSMNYEDGGICNATNDITLDGDCYIYEIRFDGVNFPANGPVMQKRTVKWEPSTEKLYVRDGVLKGDVNMALSLEGGGHYRCDFKTTYKAKKVVQLPDYHFVDHHIEIKSHDKDYSNVNLHEHAEAHS 217
               SCOP domains d3zujc_ C: automated matches                                                                                                                                                                                            SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeeeeeeeee..eeeeeeeeeeee....eeeeeeeeee......hhhhhh....--............hhhhhh....eeeeeeeee....eeeeeeeeeee..eeeeeeeeeee............eeee..eeeeeeee..eeeeeeeeeeee....eeeeeeeeeeee.........eeeeeeeeeeee.....eeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3zuj C   3 VIKPDMKIKLRMEGAVNGHPFAIEGVGLGKPFEGKQSMDLKVKEGGPLPFAYDILTMAFc--NRVFAKYPENIVDYFKQSFPEGYSWERSMIYEDGGICNATNDITLDGDCYIYEIRFDGVNFPANGPVMQKRTVKWELSTEKLYVRDGVLKSDGNYALSLEGGGHYRCDFKTTYKAKKVVQLPDYHSVDHHIEIKSHDKDYSNVNLHEHAEAHS 217
                                    12        22        32        42        52        63  |     72        82        92       102       112       122       132       142       152       162       172       182       192       202       212     
                                                                                     61| 65                                                                                                                                                        
                                                                                      63-GYC                                                                                                                                                       


Chain D from PDB  Type:PROTEIN  Length:212
 aligned with Q5TLG6_9CNID | Q5TLG6 from UniProtKB/TrEMBL  Length:224

    Alignment length:214
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213    
         Q5TLG6_9CNID     4 IKPDMKIKLRMEGAVNGHPFAIEGVGLGKPFEGKQSMDLKVKEGGPLPFAYDILTTVFCYGNRVFAKYPENIVDYFKQSFPEGYSWERSMNYEDGGICNATNDITLDGDCYIYEIRFDGVNFPANGPVMQKRTVKWEPSTEKLYVRDGVLKGDVNMALSLEGGGHYRCDFKTTYKAKKVVQLPDYHFVDHHIEIKSHDKDYSNVNLHEHAEAHS 217
               SCOP domains d3zujd_ D: automated matches                                                                                                                                                                                           SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeeeeeee..eeeeeeeeeeeehhh.eeeeeeeeee......hhhhhh....--............hhhhhh....eeeeeeeee....eeeeeeeeeee..eeeeeeeeeee............eeee..eeeeeeee..eeeeeeeeeeee....eeeeeeeeeeee.........eeeeeeeeeeee.....eeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3zuj D   4 IKPDMKIKLRMEGAVNGHPFAIEGVGLGKPFEGKQSMDLKVKEGGPLPFAYDILTMAFc--NRVFAKYPENIVDYFKQSFPEGYSWERSMIYEDGGICNATNDITLDGDCYIYEIRFDGVNFPANGPVMQKRTVKWELSTEKLYVRDGVLKSDGNYALSLEGGGHYRCDFKTTYKAKKVVQLPDYHSVDHHIEIKSHDKDYSNVNLHEHAEAHS 217
                                    13        23        33        43        53       ||- |      73        83        93       103       113       123       133       143       153       163       173       183       193       203       213    
                                                                                    61| 65                                                                                                                                                        
                                                                                     63-GYC                                                                                                                                                       


Chain E from PDB  Type:PROTEIN  Length:214
 aligned with Q5TLG6_9CNID | Q5TLG6 from UniProtKB/TrEMBL  Length:224

    Alignment length:216
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211      
         Q5TLG6_9CNID     2 SVIKPDMKIKLRMEGAVNGHPFAIEGVGLGKPFEGKQSMDLKVKEGGPLPFAYDILTTVFCYGNRVFAKYPENIVDYFKQSFPEGYSWERSMNYEDGGICNATNDITLDGDCYIYEIRFDGVNFPANGPVMQKRTVKWEPSTEKLYVRDGVLKGDVNMALSLEGGGHYRCDFKTTYKAKKVVQLPDYHFVDHHIEIKSHDKDYSNVNLHEHAEAHS 217
               SCOP domains d3zuje_ E: automated matches                                                                                                                                                                                             SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ......eeeeeeeeeee..eeeeeeeeeeee....eeeeeeeeee......hhhhh.....--............hhhhhh....eeeeeeeee....eeeeeeeeeee..eeeeeeeeeee............eeee..eeeeeeee..eeeeeeeeeeee....eeeeeeeeeeee.........eeeeeeeeeeee.....eeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3zuj E   2 SVIKPDMKIKLRMEGAVNGHPFAIEGVGLGKPFEGKQSMDLKVKEGGPLPFAYDILTMAFc--NRVFAKYPENIVDYFKQSFPEGYSWERSMIYEDGGICNATNDITLDGDCYIYEIRFDGVNFPANGPVMQKRTVKWELSTEKLYVRDGVLKSDGNYALSLEGGGHYRCDFKTTYKAKKVVQLPDYHSVDHHIEIKSHDKDYSNVNLHEHAEAHS 217
                                    11        21        31        41        51        61|  |    71        81        91       101       111       121       131       141       151       161       171       181       191       201       211      
                                                                                      61| 65                                                                                                                                                        
                                                                                       63-GYC                                                                                                                                                       


Chain F from PDB  Type:PROTEIN  Length:214
 aligned with Q5TLG6_9CNID | Q5TLG6 from UniProtKB/TrEMBL  Length:224

    Alignment length:216
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211      
         Q5TLG6_9CNID     2 SVIKPDMKIKLRMEGAVNGHPFAIEGVGLGKPFEGKQSMDLKVKEGGPLPFAYDILTTVFCYGNRVFAKYPENIVDYFKQSFPEGYSWERSMNYEDGGICNATNDITLDGDCYIYEIRFDGVNFPANGPVMQKRTVKWEPSTEKLYVRDGVLKGDVNMALSLEGGGHYRCDFKTTYKAKKVVQLPDYHFVDHHIEIKSHDKDYSNVNLHEHAEAHS 217
               SCOP domains d3zujf_ F: automated matches                                                                                                                                                                                             SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ......eeeeeeeeeee..eeeeeeeeeeee....eeeeeeeeee......hhhhhh....--..............hhhhh...eeeeeeeee....eeeeeeeeeee..eeeeeeeeeee............eeee..eeeeeeee..eeeeeeeeeeee....eeeeeeeeeeee.........eeeeeeeeeeee.....eeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3zuj F   2 SVIKPDMKIKLRMEGAVNGHPFAIEGVGLGKPFEGKQSMDLKVKEGGPLPFAYDILTMAFc--NRVFAKYPENIVDYFKQSFPEGYSWERSMIYEDGGICNATNDITLDGDCYIYEIRFDGVNFPANGPVMQKRTVKWELSTEKLYVRDGVLKSDGNYALSLEGGGHYRCDFKTTYKAKKVVQLPDYHSVDHHIEIKSHDKDYSNVNLHEHAEAHS 217
                                    11        21        31        41        51        61|  |    71        81        91       101       111       121       131       141       151       161       171       181       191       201       211      
                                                                                      61| 65                                                                                                                                                        
                                                                                       63-GYC
   Legend:   → Mismatch (orange background)
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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, 6)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3ZUJ)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3ZUJ)

(-) Gene Ontology  (2, 2)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D,E,F   (Q5TLG6_9CNID | Q5TLG6)
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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  3zuj
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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/TrEMBL
        Q5TLG6_9CNID | Q5TLG6: 2gx0 2gx2 2ie2 2iov 2pox 2z1o 2z6x 2z6y 2z6z 3zuf 3zul 4emq 4hq8 4hq9 4hqc 4izn 4uts 5hzs 5hzt 5hzu

(-) Related Entries Specified in the PDB File

3zuf PADRON OFF (NON-FLUORESCENT) BTRANS
3zul PADRON ON (FLUORESCENT) ICIS INTERMEDIATE STATE