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(-) Description

Title :  CRYSTAL STRUCTURE OF A SINGLE MUTANT OF DRONPA, THE GREEN-ON-STATE PDM1-4
 
Authors :  N. B. Ngan, K. Van Hecke, L. Van Meervelt
Date :  12 Apr 12  (Deposition) - 21 Nov 12  (Release) - 23 Jan 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.95
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 :  Dronpa, Gfp-Like Protein, Reversible Photoswitchable Fluorescent Protein, Beta Barrel, Fluorescent Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  N. Nguyen Bich, B. Moeyaert, K. Van Hecke, P. Dedecker, H. Mizuno, J. Hofkens, L. Van Meervelt
Structural Basis For The Influence Of A Single Mutation K145N On The Oligomerization And Photoswitching Rate Of Dronpa.
Acta Crystallogr. , Sect. D V. 68 1653 2012
PubMed-ID: 23151630  |  Reference-DOI: 10.1107/S0907444912039686

(-) Compounds

Molecule 1 - FLUORESCENT PROTEIN DRONPA
    ChainsA, B, C, D, E, F
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System StrainJM109(DE3)
    Expression System Taxid562
    GeneDRONPA
    MutationYES
    Organism ScientificECHINOPHYLLIA SP. SC22
    Organism Taxid301887

 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  (4, 20)

Asymmetric Unit (4, 20)
No.NameCountTypeFull Name
11PE1Ligand/IonPENTAETHYLENE GLYCOL
2EPE6Ligand/Ion4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
3GYC6Mod. Amino Acid[(4Z)-2-[(1R)-1-AMINO-2-MERCAPTOETHYL]-4-(4-HYDROXYBENZYLIDENE)-5-OXO-4,5-DIHYDRO-1H-IMIDAZOL-1-YL]ACETIC ACID
4PEG7Ligand/IonDI(HYDROXYETHYL)ETHER
Biological Unit 1 (3, 3)
No.NameCountTypeFull Name
11PE1Ligand/IonPENTAETHYLENE GLYCOL
2EPE1Ligand/Ion4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
3GYC1Mod. Amino Acid[(4Z)-2-[(1R)-1-AMINO-2-MERCAPTOETHYL]-4-(4-HYDROXYBENZYLIDENE)-5-OXO-4,5-DIHYDRO-1H-IMIDAZOL-1-YL]ACETIC ACID
4PEG-1Ligand/IonDI(HYDROXYETHYL)ETHER
Biological Unit 2 (3, 3)
No.NameCountTypeFull Name
11PE-1Ligand/IonPENTAETHYLENE GLYCOL
2EPE1Ligand/Ion4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
3GYC1Mod. Amino Acid[(4Z)-2-[(1R)-1-AMINO-2-MERCAPTOETHYL]-4-(4-HYDROXYBENZYLIDENE)-5-OXO-4,5-DIHYDRO-1H-IMIDAZOL-1-YL]ACETIC ACID
4PEG1Ligand/IonDI(HYDROXYETHYL)ETHER
Biological Unit 3 (3, 4)
No.NameCountTypeFull Name
11PE-1Ligand/IonPENTAETHYLENE GLYCOL
2EPE1Ligand/Ion4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
3GYC1Mod. Amino Acid[(4Z)-2-[(1R)-1-AMINO-2-MERCAPTOETHYL]-4-(4-HYDROXYBENZYLIDENE)-5-OXO-4,5-DIHYDRO-1H-IMIDAZOL-1-YL]ACETIC ACID
4PEG2Ligand/IonDI(HYDROXYETHYL)ETHER
Biological Unit 4 (3, 3)
No.NameCountTypeFull Name
11PE-1Ligand/IonPENTAETHYLENE GLYCOL
2EPE1Ligand/Ion4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
3GYC1Mod. Amino Acid[(4Z)-2-[(1R)-1-AMINO-2-MERCAPTOETHYL]-4-(4-HYDROXYBENZYLIDENE)-5-OXO-4,5-DIHYDRO-1H-IMIDAZOL-1-YL]ACETIC ACID
4PEG1Ligand/IonDI(HYDROXYETHYL)ETHER
Biological Unit 5 (3, 3)
No.NameCountTypeFull Name
11PE-1Ligand/IonPENTAETHYLENE GLYCOL
2EPE1Ligand/Ion4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
3GYC1Mod. Amino Acid[(4Z)-2-[(1R)-1-AMINO-2-MERCAPTOETHYL]-4-(4-HYDROXYBENZYLIDENE)-5-OXO-4,5-DIHYDRO-1H-IMIDAZOL-1-YL]ACETIC ACID
4PEG1Ligand/IonDI(HYDROXYETHYL)ETHER
Biological Unit 6 (3, 4)
No.NameCountTypeFull Name
11PE-1Ligand/IonPENTAETHYLENE GLYCOL
2EPE1Ligand/Ion4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
3GYC1Mod. Amino Acid[(4Z)-2-[(1R)-1-AMINO-2-MERCAPTOETHYL]-4-(4-HYDROXYBENZYLIDENE)-5-OXO-4,5-DIHYDRO-1H-IMIDAZOL-1-YL]ACETIC ACID
4PEG2Ligand/IonDI(HYDROXYETHYL)ETHER

(-) Sites  (12, 12)

Asymmetric Unit (12, 12)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREARG A:149 , ASP A:150 , GLY A:165 , GLY A:167 , HOH A:422 , HOH A:465 , HOH A:483 , HIS C:200BINDING SITE FOR RESIDUE EPE A 301
02AC2SOFTWAREASP A:41 , LYS A:43 , ASN A:206 , ASP F:150 , GLY F:151 , VAL F:152BINDING SITE FOR RESIDUE 1PE A 302
03AC3SOFTWAREVAL B:148 , ARG B:149 , ASP B:150 , GLY B:167 , HOH B:416 , HOH B:468 , HOH B:471 , HOH B:481BINDING SITE FOR RESIDUE EPE B 301
04AC4SOFTWAREASP B:150 , GLY B:151BINDING SITE FOR RESIDUE PEG B 302
05AC5SOFTWAREPRO A:51 , VAL C:148 , ARG C:149 , ASP C:150 , HOH C:427 , HOH C:428 , GLY D:165 , GLY D:167BINDING SITE FOR RESIDUE EPE C 301
06AC6SOFTWAREHOH C:538 , HOH C:541BINDING SITE FOR RESIDUE PEG C 302
07AC7SOFTWAREVAL A:152 , HOH A:457 , LYS C:43BINDING SITE FOR RESIDUE PEG C 303
08AC8SOFTWAREGLY C:167 , VAL D:148 , ARG D:149 , ASP D:150 , HOH D:413 , HOH D:423BINDING SITE FOR RESIDUE EPE D 301
09AC9SOFTWAREGLN C:81 , LYS C:181 , ASP E:150 , HOH E:414 , HOH E:474 , HOH E:535 , GLY F:165 , GLY F:167BINDING SITE FOR RESIDUE EPE E 301
10BC1SOFTWAREHOH E:458 , HOH E:459 , HOH E:535 , GLY F:167 , HIS F:168 , HOH F:416 , HOH F:489BINDING SITE FOR RESIDUE EPE F 301
11BC2SOFTWARETYR E:147 , ASP E:156 , LYS E:174 , ASN F:94 , GLU F:96 , ARG F:170 , ASP F:172 , HOH F:538 , HOH F:547BINDING SITE FOR RESIDUE PEG F 302
12BC3SOFTWAREASP C:110 , PRO F:51 , MET F:132 , LYS F:134 , HOH F:461 , HOH F:494BINDING SITE FOR RESIDUE PEG F 303

(-) SS Bonds  (0, 0)

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

(-) 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 4EMQ)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4EMQ)

(-) 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:215
                                                                                                                                                                                                                                                       
               SCOP domains d4emqa_ A: 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
                 4emq A   2 SVIKPDMKIKLRMEGAVNGHPFAIEGVGLGKPFEGKQSMDLKVKEGGPLPFAYDILTTVFcNRVFAKYPENIVDYFKQSFPEGYSWERSMNYEDGGICNATNDITLDGDCYIYEIRFDGVNFPANGPVMQKRTVKWEPSTENLYVRDGVLKGDVNMALSLEGGGHYRCDFKTTYKAKKVVQLPDYHFVDHHIEIKSHDKDYSNVNLHEHAEAHSE 218
                                    11        21        31        41        51        61||      73        83        93       103       113       123       133       143       153       163       173       183       193       203       213     
                                                                                      61||                                                                                                                                                         
                                                                                       63-GYC                                                                                                                                                      
                                                                                        65                                                                                                                                                         

Chain B from PDB  Type:PROTEIN  Length:214
                                                                                                                                                                                                                                                      
               SCOP domains d4emqb_ B: 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
                 4emq B   3 VIKPDMKIKLRMEGAVNGHPFAIEGVGLGKPFEGKQSMDLKVKEGGPLPFAYDILTTVFcNRVFAKYPENIVDYFKQSFPEGYSWERSMNYEDGGICNATNDITLDGDCYIYEIRFDGVNFPANGPVMQKRTVKWEPSTENLYVRDGVLKGDVNMALSLEGGGHYRCDFKTTYKAKKVVQLPDYHFVDHHIEIKSHDKDYSNVNLHEHAEAHSE 218
                                    12        22        32        42        52        63|       74        84        94       104       114       124       134       144       154       164       174       184       194       204       214    
                                                                                     61||                                                                                                                                                         
                                                                                      63-GYC                                                                                                                                                      
                                                                                       65                                                                                                                                                         

Chain C from PDB  Type:PROTEIN  Length:214
                                                                                                                                                                                                                                                      
               SCOP domains d4emqc_ C: automated matches                                                                                                                                                                                           SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeeeeeeeee..eeeeeeeeeeee....eeeeeeeeee......hhhhhhhhh.............hhhhhh....eeeeeeeee....eeeeeeeeeee..eeeeeeeeeee............eeee..eeeeeeee..eeeeeeeeeeee....eeeeeeeeeeee.........eeeeeeeeeeee.....eeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4emq C   2 SVIKPDMKIKLRMEGAVNGHPFAIEGVGLGKPFEGKQSMDLKVKEGGPLPFAYDILTTVFcNRVFAKYPENIVDYFKQSFPEGYSWERSMNYEDGGICNATNDITLDGDCYIYEIRFDGVNFPANGPVMQKRTVKWEPSTENLYVRDGVLKGDVNMALSLEGGGHYRCDFKTTYKAKKVVQLPDYHFVDHHIEIKSHDKDYSNVNLHEHAEAHS 217
                                    11        21        31        41        51        61||      73        83        93       103       113       123       133       143       153       163       173       183       193       203       213    
                                                                                      61||                                                                                                                                                        
                                                                                       63-GYC                                                                                                                                                     
                                                                                        65                                                                                                                                                        

Chain D from PDB  Type:PROTEIN  Length:215
                                                                                                                                                                                                                                                       
               SCOP domains d4emqd_ D: 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
                 4emq D   2 SVIKPDMKIKLRMEGAVNGHPFAIEGVGLGKPFEGKQSMDLKVKEGGPLPFAYDILTTVFcNRVFAKYPENIVDYFKQSFPEGYSWERSMNYEDGGICNATNDITLDGDCYIYEIRFDGVNFPANGPVMQKRTVKWEPSTENLYVRDGVLKGDVNMALSLEGGGHYRCDFKTTYKAKKVVQLPDYHFVDHHIEIKSHDKDYSNVNLHEHAEAHSE 218
                                    11        21        31        41        51        61||      73        83        93       103       113       123       133       143       153       163       173       183       193       203       213     
                                                                                      61||                                                                                                                                                         
                                                                                       63-GYC                                                                                                                                                      
                                                                                        65                                                                                                                                                         

Chain E from PDB  Type:PROTEIN  Length:214
                                                                                                                                                                                                                                                      
               SCOP domains d4emqe_ E: 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
                 4emq E   2 SVIKPDMKIKLRMEGAVNGHPFAIEGVGLGKPFEGKQSMDLKVKEGGPLPFAYDILTTVFcNRVFAKYPENIVDYFKQSFPEGYSWERSMNYEDGGICNATNDITLDGDCYIYEIRFDGVNFPANGPVMQKRTVKWEPSTENLYVRDGVLKGDVNMALSLEGGGHYRCDFKTTYKAKKVVQLPDYHFVDHHIEIKSHDKDYSNVNLHEHAEAHS 217
                                    11        21        31        41        51        61||      73        83        93       103       113       123       133       143       153       163       173       183       193       203       213    
                                                                                      61||                                                                                                                                                        
                                                                                       63-GYC                                                                                                                                                     
                                                                                        65                                                                                                                                                        

Chain F from PDB  Type:PROTEIN  Length:214
                                                                                                                                                                                                                                                      
               SCOP domains d4emqf_ F: 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
                 4emq F   2 SVIKPDMKIKLRMEGAVNGHPFAIEGVGLGKPFEGKQSMDLKVKEGGPLPFAYDILTTVFcNRVFAKYPENIVDYFKQSFPEGYSWERSMNYEDGGICNATNDITLDGDCYIYEIRFDGVNFPANGPVMQKRTVKWEPSTENLYVRDGVLKGDVNMALSLEGGGHYRCDFKTTYKAKKVVQLPDYHFVDHHIEIKSHDKDYSNVNLHEHAEAHS 217
                                    11        21        31        41        51        61||      73        83        93       103       113       123       133       143       153       163       173       183       193       203       213    
                                                                                      61||                                                                                                                                                        
                                                                                       63-GYC                                                                                                                                                     
                                                                                        65                                                                                                                                                        

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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

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (2, 2)

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 Related Entries

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

UniProtKB/TrEMBL
        Q5TLG6_9CNID | Q5TLG62gx0 2gx2 2ie2 2iov 2pox 2z1o 2z6x 2z6y 2z6z 3zuf 3zuj 3zul 4hq8 4hq9 4hqc 4izn 4uts 5hzs 5hzt 5hzu

(-) Related Entries Specified in the PDB File

2z1o DRONPA STRUCTURE
2z6y DRONPA STRUCTURE
2z6z DRONPA STRUCTURE