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(-) Description

Title :  CRYSTAL STRUCTURE OF A GREEN-TO-RED PHOTOCONVERTIBLE DRONPA, PCDRONPA IN THE GREEN-OFF-STATE
 
Authors :  N. Nguyen Bich, L. Van Meervelt
Date :  25 Oct 12  (Deposition) - 13 Nov 13  (Release) - 23 Apr 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.07
Chains :  Asym. Unit :  A,B,C,D,E,F
Biol. Unit 1:  A,B  (2x)
Biol. Unit 2:  C,D,E,F  (1x)
Keywords :  Green-To-Red Fluorescent Protein, Dronpa, Beta-Barrel, Fluorescent Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  B. Moeyaert, N. Nguyen Bich, E. De Zitter, S. Rocha, K. Clays, H. Mizuno, L. Van Meervelt, J. Hofkens, P. Dedecker
Green-To-Red Photoconvertible Dronpa Mutant For Multimodal Super-Resolution Fluorescence Microscopy
Acs Nano V. 8 1664 2014
PubMed-ID: 24410188  |  Reference-DOI: 10.1021/NN4060144

(-) Compounds

Molecule 1 - FLUORESCENT PROTEIN DRONPA
    Chains: A, B, C, D, E, F
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: DRONPA
    Mutation: YES
    Organism Scientific: ECHINOPHYLLIA
    Organism Taxid: 301887
    Strain: SC22
    Synonym: GREEN FLUORESCENT PROTEIN

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit : ABCDEF
Biological Unit 1 (2x): AB    
Biological Unit 2 (1x):   CDEF

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 13)

Asymmetric Unit (4, 13)
No.NameCountTypeFull Name
1CR86Mod. Amino Acid2-[1-AMINO-2-(1H-IMIDAZOL-5-YL)ETHYL]-1-(CARBOXYMETHYL)-4-[(4-OXOCYCLOHEXA-2,5-DIEN-1-YLIDENE)METHYL]-1H-IMIDAZOL-5-OLATE
2PEG4Ligand/IonDI(HYDROXYETHYL)ETHER
3PG42Ligand/IonTETRAETHYLENE GLYCOL
4PGE1Ligand/IonTRIETHYLENE GLYCOL
Biological Unit 1 (3, 10)
No.NameCountTypeFull Name
1CR84Mod. Amino Acid2-[1-AMINO-2-(1H-IMIDAZOL-5-YL)ETHYL]-1-(CARBOXYMETHYL)-4-[(4-OXOCYCLOHEXA-2,5-DIEN-1-YLIDENE)METHYL]-1H-IMIDAZOL-5-OLATE
2PEG4Ligand/IonDI(HYDROXYETHYL)ETHER
3PG4-1Ligand/IonTETRAETHYLENE GLYCOL
4PGE2Ligand/IonTRIETHYLENE GLYCOL
Biological Unit 2 (3, 8)
No.NameCountTypeFull Name
1CR84Mod. Amino Acid2-[1-AMINO-2-(1H-IMIDAZOL-5-YL)ETHYL]-1-(CARBOXYMETHYL)-4-[(4-OXOCYCLOHEXA-2,5-DIEN-1-YLIDENE)METHYL]-1H-IMIDAZOL-5-OLATE
2PEG2Ligand/IonDI(HYDROXYETHYL)ETHER
3PG42Ligand/IonTETRAETHYLENE GLYCOL
4PGE-1Ligand/IonTRIETHYLENE GLYCOL

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELEU A:12 , ARG A:13 , ILE A:115 , TYR A:116BINDING SITE FOR RESIDUE PEG A 301
2AC2SOFTWARELYS A:43 , ASN A:206 , HOH A:448 , HOH A:511 , ASP F:150 , GLY F:151 , VAL F:152BINDING SITE FOR RESIDUE PGE A 302
3AC3SOFTWARESER B:94 , GLU B:96 , ASP B:156 , ARG B:170 , ASP B:172 , LYS B:174BINDING SITE FOR RESIDUE PEG B 301
4AC4SOFTWARESER C:94 , TYR C:95 , GLU C:96 , ARG C:170 , ASP C:172 , HOH C:443 , HOH C:510 , ASP D:156 , LYS D:174 , ASP F:97 , GLY F:98BINDING SITE FOR RESIDUE PG4 C 301
5AC5SOFTWAREPRO A:49 , ASN D:128 , ARG D:135 , LEU D:163 , HOH D:485BINDING SITE FOR RESIDUE PEG D 301
6AC6SOFTWARELYS E:174 , SER F:94 , TYR F:95 , GLU F:96 , ASP F:172BINDING SITE FOR RESIDUE PEG F 301
7AC7SOFTWARESER E:94 , TYR E:95 , GLU E:96 , ARG E:170 , ASP E:172 , TYR F:147 , ASP F:156 , LYS F:174BINDING SITE FOR RESIDUE PG4 F 302

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4HQ9)

(-) Cis Peptide Bonds  (12, 12)

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
9Gly E:48 -Pro E:49
10Phe E:83 -Pro E:84
11Gly F:48 -Pro F:49
12Phe F:83 -Pro F:84

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4HQ9)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4HQ9)

(-) Exons   (0, 0)

(no "Exon" information available for 4HQ9)

(-) 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:217
                                                                                                                                                                                                                                                         
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeeeeeeeee..eeeeeeeeeee.....eeeeeeeeee......hhhhhh....hhhhh.......hhhhhh....eeeeeeeee....eeeeeeeeeee..eeeeeeeeeee............eeee..eeeeeeee..eeeeeeeeeeee....eeeeeeeeeeee.........eeeeeeeeeeee.....eeeeeeeeeee..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4hq9 A   3 VIKPDMKIKLRMEGAVNGHPFAIEGVGLGKPFEGKQSMDLKVKEGGPLPFAYDILTTAFhNRVFAKYPENIVDYFKQSFPEGYSWERSMSYEDGGICIATNDITLDGDCYIYEIRFDGVNFPANGPVMQKRTVKWEPSTEKLYVRDGVLKGDVNMALSLEGGGHYRCDFKTTYKAKKVVQLPDYHFVDHHIEIKSHDKDYSNVNLHEHAEAHSGLPR 221
                                    12        22        32        42        52        63|       74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       
                                                                                     61||                                                                                                                                                            
                                                                                      63-CR8                                                                                                                                                         
                                                                                       65                                                                                                                                                            


Chain B from PDB  Type:PROTEIN  Length:216
                                                                                                                                                                                                                                                        
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .....eeeeeeeeeee..eeeeeeeeeee.....eeeeeeeeee......hhhhhh....hhhhh.......hhhhhh....eeeeeeeee....eeeeeeeeeee..eeeeeeeeeee............eeee..eeeeeeee..eeeeeeeeeeee....eeeeeeeeeeee.........eeeeeeeeeeee.....eeeeeeeeeee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4hq9 B   3 VIKPDMKIKLRMEGAVNGHPFAIEGVGLGKPFEGKQSMDLKVKEGGPLPFAYDILTTAFhNRVFAKYPENIVDYFKQSFPEGYSWERSMSYEDGGICIATNDITLDGDCYIYEIRFDGVNFPANGPVMQKRTVKWEPSTEKLYVRDGVLKGDVNMALSLEGGGHYRCDFKTTYKAKKVVQLPDYHFVDHHIEIKSHDKDYSNVNLHEHAEAHSGLP 220
                                    12        22        32        42        52        63|       74        84        94       104       114       124       134       144       154       164       174       184       194       204       214      
                                                                                     61||                                                                                                                                                           
                                                                                      63-CR8                                                                                                                                                        
                                                                                       65                                                                                                                                                           


Chain C from PDB  Type:PROTEIN  Length:218
                                                                                                                                                                                                                                                          
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeeeeeeeee..eeeeeeeeeeee....eeeeeeeeee......hhhhhhhhh.hhhhh.......hhhhhh....eeeeeeeee....eeeeeeeeeee..eeeeeeeeeee............eeee..eeeeeeee..eeeeeeeeeeee....eeeeeeeeeeee.........eeeeeeeeeeee.....eeeeeeeeeee.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4hq9 C   1 MSVIKPDMKIKLRMEGAVNGHPFAIEGVGLGKPFEGKQSMDLKVKEGGPLPFAYDILTTAFhNRVFAKYPENIVDYFKQSFPEGYSWERSMSYEDGGICIATNDITLDGDCYIYEIRFDGVNFPANGPVMQKRTVKWEPSTEKLYVRDGVLKGDVNMALSLEGGGHYRCDFKTTYKAKKVVQLPDYHFVDHHIEIKSHDKDYSNVNLHEHAEAHSGLP 220
                                    10        20        30        40        50        60|||     72        82        92       102       112       122       132       142       152       162       172       182       192       202       212        
                                                                                       61||                                                                                                                                                           
                                                                                        63-CR8                                                                                                                                                        
                                                                                         65                                                                                                                                                           


Chain D from PDB  Type:PROTEIN  Length:216
                                                                                                                                                                                                                                                        
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .....eeeeeeeeeee..eeeeeeeeeeee....eeeeeeeeee......hhhhhh....hhhhh.......hhhhhh....eeeeeeeee....eeeeeeeeeee..eeeeeeeeeee............eeee..eeeeeeee..eeeeeeeeeeee....eeeeeeeeeeee.........eeeeeeeeeeee.....eeeeeeeeeee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4hq9 D   3 VIKPDMKIKLRMEGAVNGHPFAIEGVGLGKPFEGKQSMDLKVKEGGPLPFAYDILTTAFhNRVFAKYPENIVDYFKQSFPEGYSWERSMSYEDGGICIATNDITLDGDCYIYEIRFDGVNFPANGPVMQKRTVKWEPSTEKLYVRDGVLKGDVNMALSLEGGGHYRCDFKTTYKAKKVVQLPDYHFVDHHIEIKSHDKDYSNVNLHEHAEAHSGLP 220
                                    12        22        32        42        52        63|       74        84        94       104       114       124       134       144       154       164       174       184       194       204       214      
                                                                                     61||                                                                                                                                                           
                                                                                      63-CR8                                                                                                                                                        
                                                                                       65                                                                                                                                                           


Chain E from PDB  Type:PROTEIN  Length:217
                                                                                                                                                                                                                                                         
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeeeeeeeee..eeeeeeeeeeee....eeeeeeeeee......hhhhhhhhh.hhhhh.......hhhhhh....eeeeeeeee....eeeeeeeeeee..eeeeeeeeeee............eeee..eeeeeeee..eeeeeeeeeeee....eeeeeeeeeeee.........eeeeeeeeeeee.....eeeeeeeeeee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4hq9 E   2 SVIKPDMKIKLRMEGAVNGHPFAIEGVGLGKPFEGKQSMDLKVKEGGPLPFAYDILTTAFhNRVFAKYPENIVDYFKQSFPEGYSWERSMSYEDGGICIATNDITLDGDCYIYEIRFDGVNFPANGPVMQKRTVKWEPSTEKLYVRDGVLKGDVNMALSLEGGGHYRCDFKTTYKAKKVVQLPDYHFVDHHIEIKSHDKDYSNVNLHEHAEAHSGLP 220
                                    11        21        31        41        51        61||      73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       
                                                                                      61||                                                                                                                                                           
                                                                                       63-CR8                                                                                                                                                        
                                                                                        65                                                                                                                                                           


Chain F from PDB  Type:PROTEIN  Length:214
                                                                                                                                                                                                                                                      
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeeeeeeeee..eeeeeeeeeeee....eeeeeeeeee......hhhhhhhhh.hhhhh.......hhhhhh....eeeeeeeee....eeeeeeeeeee..eeeeeeeeeee............eeee..eeeeeeee..eeeeeeeeeeee....eeeeeeeeeeee.........eeeeeeeeeeee.....eeeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4hq9 F   3 VIKPDMKIKLRMEGAVNGHPFAIEGVGLGKPFEGKQSMDLKVKEGGPLPFAYDILTTAFhNRVFAKYPENIVDYFKQSFPEGYSWERSMSYEDGGICIATNDITLDGDCYIYEIRFDGVNFPANGPVMQKRTVKWEPSTEKLYVRDGVLKGDVNMALSLEGGGHYRCDFKTTYKAKKVVQLPDYHFVDHHIEIKSHDKDYSNVNLHEHAEAHSG 218
                                    12        22        32        42        52        63|       74        84        94       104       114       124       134       144       154       164       174       184       194       204       214    
                                                                                     61||                                                                                                                                                         
                                                                                      63-CR8                                                                                                                                                      
                                                                                       65
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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 4HQ9)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4HQ9)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4HQ9)

(-) Gene Ontology  (2, 2)

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 Related Entries

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

(-) Related Entries Specified in the PDB File

4hq8 THE SAME PROTEIN
4hqc