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(-) Description

Title :  1.95 ANGSTROM CRYSTAL STRUCTURE OF TAGRFP-T
 
Authors :  X. J. Hu
Date :  11 May 16  (Deposition) - 17 May 17  (Release) - 17 May 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.95
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Red Fluorescent Proteins, Tagrfp-T, Beta Barrel, Photostable, Fluorescent Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. Liu, Q. N. Liang, S. Q. Du, X. J. Hu, Y. Ding
The Crystal Structure Of Red Fluorescent Protein Tagrfp-T Reveals The Mechanism Of Its Superior Photostability.
Biochem. Biophys. Res. V. 477 229 2016 Commun.
PubMed-ID: 27297107  |  Reference-DOI: 10.1016/J.BBRC.2016.06.047

(-) Compounds

Molecule 1 - TAGRFP-T
    Chains: A, B, C, D
    Engineered: YES
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630
    Synthetic: YES

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 10)

Asymmetric/Biological Unit (3, 10)
No.NameCountTypeFull Name
1BME4Ligand/IonBETA-MERCAPTOETHANOL
2NRQ4Mod. Amino Acid{(4Z)-4-(4-HYDROXYBENZYLIDENE)-2-[3-(METHYLTHIO)PROPANIMIDOYL]-5-OXO-4,5-DIHYDRO-1H-IMIDAZOL-1-YL}ACETIC ACID
3SO42Ligand/IonSULFATE ION

(-) Sites  (18, 18)

Asymmetric Unit (18, 18)
No.NameEvidenceResiduesDescription
01AC1SOFTWARETYR A:194 , ARG A:220 , CYS A:222 , ASN B:143 , THR B:144 , ASP B:196binding site for residue BME A 301
02AC2SOFTWARETYR A:221 , CYS A:222 , ARG B:198 , LYS B:207 , HOH B:410binding site for residue SO4 B 301
03AC3SOFTWAREASN A:143 , THR A:144 , TYR B:194 , ARG B:220 , CYS B:222binding site for residue BME B 302
04AC4SOFTWARETYR C:194 , ARG C:220 , CYS C:222 , ASN D:143 , THR D:144binding site for residue BME C 301
05AC5SOFTWARELYS A:207 , TYR C:221 , CYS C:222 , ARG D:198binding site for residue SO4 C 302
06AC6SOFTWAREASN C:143 , THR C:144 , ASP C:196 , TYR D:194 , ARG D:220 , CYS D:222binding site for residue BME D 301
07AC7SOFTWARELEU B:13 , MET B:15 , MET B:41 , ILE B:43 , PHE B:55 , LEU B:58 , ALA B:59 , THR B:60 , SER B:61 , SER B:66 , ARG B:67 , TRP B:90 , ARG B:92 , GLN B:106 , ASN B:143 , GLU B:145 , THR B:158 , MET B:160 , PHE B:174 , HIS B:197 , LEU B:199 , GLN B:213 , GLU B:215 , HOH B:408 , HOH B:416 , HOH B:420 , HOH B:425binding site for Di-peptide PHE B 62 and NRQ B 64
08AC8SOFTWARELEU B:13 , MET B:15 , MET B:41 , ILE B:43 , PHE B:55 , LEU B:58 , ALA B:59 , THR B:60 , SER B:61 , SER B:66 , ARG B:67 , TRP B:90 , ARG B:92 , GLN B:106 , ASN B:143 , GLU B:145 , THR B:158 , MET B:160 , PHE B:174 , HIS B:197 , LEU B:199 , GLN B:213 , GLU B:215 , HOH B:408 , HOH B:416 , HOH B:420 , HOH B:425binding site for Di-peptide PHE B 62 and NRQ B 64
09AC9SOFTWAREGLN B:39 , ALA B:59 , THR B:60 , SER B:61 , PHE B:62 , ARG B:67 , THR B:68 , PHE B:69 , TRP B:90 , ARG B:92 , GLN B:106 , TYR B:117 , ASN B:143 , GLU B:145 , THR B:158 , MET B:160 , PHE B:174 , HIS B:197 , LEU B:199 , GLN B:213 , GLU B:215 , HOH B:408 , HOH B:416 , HOH B:420 , HOH B:425binding site for Di-peptide NRQ B 64 and SER B 66
10AD1SOFTWAREGLN B:39 , ALA B:59 , THR B:60 , SER B:61 , PHE B:62 , ARG B:67 , THR B:68 , PHE B:69 , TRP B:90 , ARG B:92 , GLN B:106 , TYR B:117 , ASN B:143 , GLU B:145 , THR B:158 , MET B:160 , PHE B:174 , HIS B:197 , LEU B:199 , GLN B:213 , GLU B:215 , HOH B:408 , HOH B:416 , HOH B:420 , HOH B:425binding site for Di-peptide NRQ B 64 and SER B 66
11AD2SOFTWARELEU C:13 , MET C:15 , GLN C:39 , MET C:41 , ILE C:43 , PHE C:55 , LEU C:58 , ALA C:59 , THR C:60 , SER C:61 , SER C:66 , ARG C:67 , TRP C:90 , ARG C:92 , GLN C:106 , ASN C:143 , GLU C:145 , THR C:158 , MET C:160 , PHE C:174 , HIS C:197 , LEU C:199 , GLN C:213 , GLU C:215 , HOH C:405 , HOH C:419 , HOH C:429binding site for Di-peptide PHE C 62 and NRQ C 64
12AD3SOFTWARELEU C:13 , MET C:15 , GLN C:39 , MET C:41 , ILE C:43 , PHE C:55 , LEU C:58 , ALA C:59 , THR C:60 , SER C:61 , SER C:66 , ARG C:67 , TRP C:90 , ARG C:92 , GLN C:106 , ASN C:143 , GLU C:145 , THR C:158 , MET C:160 , PHE C:174 , HIS C:197 , LEU C:199 , GLN C:213 , GLU C:215 , HOH C:405 , HOH C:419 , HOH C:429binding site for Di-peptide PHE C 62 and NRQ C 64
13AD4SOFTWAREMET C:11 , GLN C:39 , MET C:41 , ALA C:59 , THR C:60 , SER C:61 , PHE C:62 , ARG C:67 , THR C:68 , PHE C:69 , TRP C:90 , ARG C:92 , GLN C:106 , TYR C:117 , ASN C:143 , GLU C:145 , THR C:158 , MET C:160 , PHE C:174 , HIS C:197 , LEU C:199 , GLN C:213 , GLU C:215 , HOH C:405 , HOH C:419 , HOH C:429binding site for Di-peptide NRQ C 64 and SER C 66
14AD5SOFTWAREMET C:11 , GLN C:39 , MET C:41 , ALA C:59 , THR C:60 , SER C:61 , PHE C:62 , ARG C:67 , THR C:68 , PHE C:69 , TRP C:90 , ARG C:92 , GLN C:106 , TYR C:117 , ASN C:143 , GLU C:145 , THR C:158 , MET C:160 , PHE C:174 , HIS C:197 , LEU C:199 , GLN C:213 , GLU C:215 , HOH C:405 , HOH C:419 , HOH C:429binding site for Di-peptide NRQ C 64 and SER C 66
15AD6SOFTWARELEU D:13 , MET D:15 , GLN D:39 , MET D:41 , ILE D:43 , PHE D:55 , LEU D:58 , ALA D:59 , THR D:60 , SER D:61 , SER D:66 , ARG D:67 , TRP D:90 , ARG D:92 , GLN D:106 , ASN D:143 , GLU D:145 , THR D:158 , MET D:160 , PHE D:174 , HIS D:197 , LEU D:199 , GLN D:213 , GLU D:215 , HOH D:406 , HOH D:409 , HOH D:435 , HOH D:447binding site for Di-peptide PHE D 62 and NRQ D 64
16AD7SOFTWARELEU D:13 , MET D:15 , GLN D:39 , MET D:41 , ILE D:43 , PHE D:55 , LEU D:58 , ALA D:59 , THR D:60 , SER D:61 , SER D:66 , ARG D:67 , TRP D:90 , ARG D:92 , GLN D:106 , ASN D:143 , GLU D:145 , THR D:158 , MET D:160 , PHE D:174 , HIS D:197 , LEU D:199 , GLN D:213 , GLU D:215 , HOH D:406 , HOH D:409 , HOH D:435 , HOH D:447binding site for Di-peptide PHE D 62 and NRQ D 64
17AD8SOFTWAREMET D:11 , GLN D:39 , MET D:41 , ALA D:59 , THR D:60 , SER D:61 , PHE D:62 , ARG D:67 , THR D:68 , PHE D:69 , TRP D:90 , ARG D:92 , GLN D:106 , TYR D:117 , ASN D:143 , GLU D:145 , THR D:158 , MET D:160 , PHE D:174 , HIS D:197 , LEU D:199 , GLN D:213 , GLU D:215 , HOH D:406 , HOH D:409 , HOH D:435 , HOH D:447binding site for Di-peptide NRQ D 64 and SER D 66
18AD9SOFTWAREMET D:11 , GLN D:39 , MET D:41 , ALA D:59 , THR D:60 , SER D:61 , PHE D:62 , ARG D:67 , THR D:68 , PHE D:69 , TRP D:90 , ARG D:92 , GLN D:106 , TYR D:117 , ASN D:143 , GLU D:145 , THR D:158 , MET D:160 , PHE D:174 , HIS D:197 , LEU D:199 , GLN D:213 , GLU D:215 , HOH D:406 , HOH D:409 , HOH D:435 , HOH D:447binding site for Di-peptide NRQ D 64 and SER D 66

(-) SS Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1A:222 -A:301
2B:222 -B:302
3C:222 -C:301
4D:222 -D:301

(-) Cis Peptide Bonds  (8, 8)

Asymmetric/Biological 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 5JVA)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5JVA)

(-) Exons   (0, 0)

(no "Exon" information available for 5JVA)

(-) Sequences/Alignments

Asymmetric/Biological 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:226
                                                                                                                                                                                                                                                                  
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eeeeeeeeeee..eeeeeeeeeeee....eeeeeeeeee......hhhhhhhhh......ee.......hhhhh...eeeeeeeee....eeeeeeeeeee..eeeeeeeeeee............eeee..eeeeeeee..eeeeeeeeeeee....eeeeeeeeeeee..hhhhh.....eeeeeeeeeeeee....eeeeeeeeeee........ Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5jva A   1 GEELIKENMHMKLYMEGTVNNHHFKCTSEGEGKPYEGTQTMRIKVVEGGPLPFAFDILATSFxSRTFINHTQGIPDFFKQSFPEGFTWERVTTYEDGGVLTATQDTSLQDGCLIYNVKIRGVNFPSNGPVMQKKTLGWEANTEMLYPADGGLEGRTDMALKLVGGGHLICNFKTTYRSKKPAKNLKMPGVYYVDHRLERIKEADKETYVEQHEVAVARYCDLPSKL 228
                                    10        20        30        40        50        60 |||    72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222      
                                                                                        62||                                                                                                                                                                  
                                                                                         64-NRQ                                                                                                                                                               
                                                                                          66                                                                                                                                                                  


Chain B from PDB  Type:PROTEIN  Length:225
                                                                                                                                                                                                                                                                 
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeeeeeeeee..eeeeeeeeeeee....eeeeeeeeee......hhhhhhhhh.hhhhhee.......hhhhh...eeeeeeeee....eeeeeeeeeee..eeeeeeeeeee............eeee..eeeeeeee..eeeeeeeeeeee....eeeeeeeeeeee..hhhhh.....eeeeeeeeeeeee....eeeeeeeeeee........ Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5jva B   2 EELIKENMHMKLYMEGTVNNHHFKCTSEGEGKPYEGTQTMRIKVVEGGPLPFAFDILATSFxSRTFINHTQGIPDFFKQSFPEGFTWERVTTYEDGGVLTATQDTSLQDGCLIYNVKIRGVNFPSNGPVMQKKTLGWEANTEMLYPADGGLEGRTDMALKLVGGGHLICNFKTTYRSKKPAKNLKMPGVYYVDHRLERIKEADKETYVEQHEVAVARYCDLPSKL 228
                                    11        21        31        41        51        61|||     73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223     
                                                                                       62||                                                                                                                                                                  
                                                                                        64-NRQ                                                                                                                                                               
                                                                                         66                                                                                                                                                                  


Chain C from PDB  Type:PROTEIN  Length:226
                                                                                                                                                                                                                                                                  
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhh...eeeeeeeeeee..eeeeeeeeeeee....eeeeeeeeee......hhhhhhhhh......ee.....hhhhhh....eeeeeeeee....eeeeeeeeeee..eeeeeeeeeee............eeee..eeeeeeee..eeeeeeeeeeee....eeeeeeeeeeee..hhhhh.....eeeeeeeeeeeee....eeeeeeeeeee........ Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5jva C   1 GEELIKENMHMKLYMEGTVNNHHFKCTSEGEGKPYEGTQTMRIKVVEGGPLPFAFDILATSFxSRTFINHTQGIPDFFKQSFPEGFTWERVTTYEDGGVLTATQDTSLQDGCLIYNVKIRGVNFPSNGPVMQKKTLGWEANTEMLYPADGGLEGRTDMALKLVGGGHLICNFKTTYRSKKPAKNLKMPGVYYVDHRLERIKEADKETYVEQHEVAVARYCDLPSKL 228
                                    10        20        30        40        50        60 |||    72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222      
                                                                                        62||                                                                                                                                                                  
                                                                                         64-NRQ                                                                                                                                                               
                                                                                          66                                                                                                                                                                  


Chain D from PDB  Type:PROTEIN  Length:223
                                                                                                                                                                                                                                                               
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeeeeeeeee..eeeeeeeeeeee....eeeeeeeeee.......hhhhhh........ee.......hhhhh...eeeeeeeee....eeeeeeeeeee..eeeeeeeeeee............eeee..eeeeeeee..eeeeeeeeeeee....eeeeeeeeeeee..hhhhh.....eeeeeeeeeeeee....eeeeeeeeeee........ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5jva D   4 LIKENMHMKLYMEGTVNNHHFKCTSEGEGKPYEGTQTMRIKVVEGGPLPFAFDILATSFxSRTFINHTQGIPDFFKQSFPEGFTWERVTTYEDGGVLTATQDTSLQDGCLIYNVKIRGVNFPSNGPVMQKKTLGWEANTEMLYPADGGLEGRTDMALKLVGGGHLICNFKTTYRSKKPAKNLKMPGVYYVDHRLERIKEADKETYVEQHEVAVARYCDLPSKL 228
                                    13        23        33        43        53        64|       75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225   
                                                                                     62||                                                                                                                                                                  
                                                                                      64-NRQ                                                                                                                                                               
                                                                                       66
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  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 5JVA)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5JVA)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5JVA)

(-) Gene Ontology  (0, 0)

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  Cis Peptide Bonds
    Gly A:49 - Pro A:50   [ RasMol ]  
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    Gly C:49 - Pro C:50   [ RasMol ]  
    Gly D:49 - Pro D:50   [ RasMol ]  
    Phe A:84 - Pro A:85   [ RasMol ]  
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3t6h THE SAME PROTEIN WITH RESOLUTION 2.20 ANGSTROM. THE CHROMPHORE IS INTERPRETED DIFFERENTLY AND MORE PRECISELY.