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(-) Description

Title :  CRYSTAL STRUCTURE OF MONOMERIC REVERSIBLY PHOTOSWITCHABLE RED FLUORESCENT PROTEIN RSTAGRFP IN THE OFF STATE
 
Authors :  S. Pletnev
Date :  16 Oct 11  (Deposition) - 22 Feb 12  (Release) - 09 May 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.78
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 :  Beta-Barrel, Fluorescent Protein, Light Induced Reversible Photoswitching, Reversibly Photoswitchable Fluorescent Protein, Cis- Trans Isomerization (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Pletnev, F. V. Subach, Z. Dauter, A. Wlodawer, V. V. Verkhusha
A Structural Basis For Reversible Photoswitching Of Absorbance Spectra In Red Fluorescent Protein Rstagrfp.
J. Mol. Biol. V. 417 144 2012
PubMed-ID: 22310052  |  Reference-DOI: 10.1016/J.JMB.2012.01.044

(-) Compounds

Molecule 1 - FLUORESCENT PROTEIN RSTAGRFP
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: XL1 BLUE
    Expression System Taxid: 562
    Expression System Vector Type: PQE30
    Organism Common: ARTIFICIAL GENE
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630

 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  (1, 4)

Asymmetric Unit (1, 4)
No.NameCountTypeFull Name
1NRQ4Mod. Amino Acid{(4Z)-4-(4-HYDROXYBENZYLIDENE)-2-[3-(METHYLTHIO)PROPANIMIDOYL]-5-OXO-4,5-DIHYDRO-1H-IMIDAZOL-1-YL}ACETIC ACID
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1NRQ1Mod. Amino Acid{(4Z)-4-(4-HYDROXYBENZYLIDENE)-2-[3-(METHYLTHIO)PROPANIMIDOYL]-5-OXO-4,5-DIHYDRO-1H-IMIDAZOL-1-YL}ACETIC ACID
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1NRQ1Mod. Amino Acid{(4Z)-4-(4-HYDROXYBENZYLIDENE)-2-[3-(METHYLTHIO)PROPANIMIDOYL]-5-OXO-4,5-DIHYDRO-1H-IMIDAZOL-1-YL}ACETIC ACID
Biological Unit 3 (1, 1)
No.NameCountTypeFull Name
1NRQ1Mod. Amino Acid{(4Z)-4-(4-HYDROXYBENZYLIDENE)-2-[3-(METHYLTHIO)PROPANIMIDOYL]-5-OXO-4,5-DIHYDRO-1H-IMIDAZOL-1-YL}ACETIC ACID
Biological Unit 4 (1, 1)
No.NameCountTypeFull Name
1NRQ1Mod. Amino Acid{(4Z)-4-(4-HYDROXYBENZYLIDENE)-2-[3-(METHYLTHIO)PROPANIMIDOYL]-5-OXO-4,5-DIHYDRO-1H-IMIDAZOL-1-YL}ACETIC ACID

(-) Sites  (0, 0)

(no "Site" information available for 3U8A)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3U8A)

(-) Cis Peptide Bonds  (8, 8)

Asymmetric Unit
No.Residues
1Gly A:49 -Pro A:50
2Phe A:84 -Pro A:85
3Gly B:49 -Pro B:50
4Phe B:84 -Pro B:85
5Gly C:49 -Pro C:50
6Phe C:84 -Pro C:85
7Gly D:49 -Pro D:50
8Phe D:84 -Pro D:85

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3U8A)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3U8A)

(-) Exons   (0, 0)

(no "Exon" information available for 3U8A)

(-) 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:224
                                                                                                                                                                                                                                                                
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeeeeeeeee..eeeeeeeeeeee....eeeeeeeeee......hhhhhhhhh.hhhhhee.....hhhhhh....eeeeeeeee....eeeeeeeeeee..eeeeeeeeeee............eeee..eeeeeeee..eeeeeeeeeeee....eeeeeeeeeeee............eeeeeeeeeeeee....eeeeeeeeeee........ Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3u8a A   3 ELIKENMHMKLYMEGTVNNHHFKCTSEGEGKPYEGTQTMRIKVVEGGPLPFAFDILATSFmSRTFINHTQGIPDFWKQSFPEGFTWERVTTYEDGGVLTATQDTSLQDGCLIYNVKLRGVNFPSNGPVMQKKTLGWEAATEMLYPADGGLEGRGDMALKLVGGGHLICNLKTTYRSKNPAKNLKMPGVYFVDHRLERIKEADKETYVEQHEVAVARYCDLPSKL 228
                                    12        22        32        42        52        62||      74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224    
                                                                                       63-NRQ                                                                                                                                                               
                                                                                        66                                                                                                                                                                  


Chain B from PDB  Type:PROTEIN  Length:224
                                                                                                                                                                                                                                                                
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeeeeeeeee..eeeeeeeeeeee....eeeeeeeeee......hhhhhhhhh......ee...............eeeeeeeee....eeeeeeeeeee..eeeeeeeeeee............eeee..eeeeeeee..eeeeeeeeeeee....eeeeeeeeeeee............eeeeeeeeeeeee....eeeeeeeeeee........ Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3u8a B   3 ELIKENMHMKLYMEGTVNNHHFKCTSEGEGKPYEGTQTMRIKVVEGGPLPFAFDILATSFmSRTFINHTQGIPDFWKQSFPEGFTWERVTTYEDGGVLTATQDTSLQDGCLIYNVKLRGVNFPSNGPVMQKKTLGWEAATEMLYPADGGLEGRGDMALKLVGGGHLICNLKTTYRSKNPAKNLKMPGVYFVDHRLERIKEADKETYVEQHEVAVARYCDLPSKL 228
                                    12        22        32        42        52        62||      74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224    
                                                                                       63-NRQ                                                                                                                                                               
                                                                                        66                                                                                                                                                                  


Chain C from PDB  Type:PROTEIN  Length:224
                                                                                                                                                                                                                                                                
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeeeeeeeee..eeeeeeeeeeee....eeeeeeeeee......hhhhhhhhh.hhhhhee...............eeeeeeeee....eeeeeeeeeee..eeeeeeeeeee............eeee..eeeeeeee..eeeeeeeeeeee....eeeeeeeeeeee............eeeeeeeeeeeee....eeeeeeeeeee........ Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3u8a C   3 ELIKENMHMKLYMEGTVNNHHFKCTSEGEGKPYEGTQTMRIKVVEGGPLPFAFDILATSFmSRTFINHTQGIPDFWKQSFPEGFTWERVTTYEDGGVLTATQDTSLQDGCLIYNVKLRGVNFPSNGPVMQKKTLGWEAATEMLYPADGGLEGRGDMALKLVGGGHLICNLKTTYRSKNPAKNLKMPGVYFVDHRLERIKEADKETYVEQHEVAVARYCDLPSKL 228
                                    12        22        32        42        52        62||      74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224    
                                                                                       63-NRQ                                                                                                                                                               
                                                                                        66                                                                                                                                                                  


Chain D from PDB  Type:PROTEIN  Length:224
                                                                                                                                                                                                                                                                
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeeeeeeeee..eeeeeeeeeeee....eeeeeeeeee......hhhhhhhhh.hhhhhee.....hhhhhh....eeeeeeeee....eeeeeeeeeee..eeeeeeeeeee............eeee..eeeeeee....eeeeeeeeeee....eeeeeeeeeeee............eeeeeeeeeeeee....eeeeeeeeeee........ Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3u8a D   3 ELIKENMHMKLYMEGTVNNHHFKCTSEGEGKPYEGTQTMRIKVVEGGPLPFAFDILATSFmSRTFINHTQGIPDFWKQSFPEGFTWERVTTYEDGGVLTATQDTSLQDGCLIYNVKLRGVNFPSNGPVMQKKTLGWEAATEMLYPADGGLEGRGDMALKLVGGGHLICNLKTTYRSKNPAKNLKMPGVYFVDHRLERIKEADKETYVEQHEVAVARYCDLPSKL 228
                                    12        22        32        42        52        62||      74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224    
                                                                                       63-NRQ                                                                                                                                                               
                                                                                        66
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    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  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  (0, 0)

(no "SCOP Domain" information available for 3U8A)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3U8A)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3U8A)

(-) Gene Ontology  (0, 0)

Asymmetric Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 3U8A)

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  Cis Peptide Bonds
    Gly A:49 - Pro A:50   [ RasMol ]  
    Gly B:49 - Pro B:50   [ RasMol ]  
    Gly C:49 - Pro C:50   [ RasMol ]  
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(-) Related Entries Specified in the PDB File

3m22 CRYSTAL STRUCTURE OF TAGRFP FLUORESCENT PROTEIN
3u8c MONOMERIC RED REVERSIBLY PHOTOSWITCHABLE FLUORESCENT PROTEIN IN THE "ON" STATE