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(-) Description

Title :  CRYSTAL STRUCTURE ANALYSIS OF THE FLUORESCENT PROTEIN KILLERRED
 
Authors :  N. Sakai, Y. Kitago, K. Takemoto, T. Matsuda, T. Nagai
Date :  08 Oct 09  (Deposition) - 14 Apr 10  (Release) - 14 Apr 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.90
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Fluorescent Protein, Phototoxicity (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  N. Sakai, K. Takemoto, T. Matsuda, Y. Kitago, T. Ayabe, T. Nagai
Crystal Structure Analysis Of The Fluorescent Protein Killerred
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - KILLERRED
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET-28A-KILLERRED
    Expression System Strain: JM109(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Organism Scientific: ANTHOMEDUSAE
    Organism Taxid: 328397
    Strain: DC-2005

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric/Biological Unit (1, 2)
No.NameCountTypeFull Name
1CRQ2Mod. Amino Acid[2-(3-CARBAMOYL-1-IMINO-PROPYL)-4-(4-HYDROXY-BENZYLIDENE)-5-OXO-4,5-DIHYDRO-IMIDAZOL-1-YL]-ACETICACID

(-) Sites  (0, 0)

(no "Site" information available for 3A8S)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3A8S)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Phe A:37 -Pro A:38
2Phe A:86 -Pro A:87
3Phe B:37 -Pro B:38
4Phe B:86 -Pro B:87

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3A8S)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3A8S)

(-) Exons   (0, 0)

(no "Exon" information available for 3A8S)

(-) 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:221
 aligned with Q2TCH5_9CNID | Q2TCH5 from UniProtKB/TrEMBL  Length:237

    Alignment length:223
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226   
         Q2TCH5_9CNID     7 LFQSDMTFKIFIDGEVNGQKFTIVADGSSKFPHGDFNVHAVCETGKLPMSWKPICHLIQYGEPFFARYPDGISHFAQECFPEGLSIDRTVRFENDGTMTSHHTYELDDTCVVSRITVNCDGFQPDGPIMRDQLVDILPNETHMFPHGPNAVRQLAFIGFTTADGGLMMGHFDSKMTFNGSRAIEIPGPHFVTIITKQMRDTSDKRDHVCQREVAYAHSVPRIT 229
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeeeeeeeee..eeeeeeeeeee.....eeeeeeee........hhhhh....--hhhhh.......hhhhhh....eeeeeeeee....eeeeeeeeeee..eeeeeeeeeee..................eeeeeeee...eeeeeeeeeee.....eeeeeeeeeeee...........eeeeeeeeeee.......eeeeeeeeeee...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3a8s A   7 LFQSDMTFKIFIDGEVNGQKFTIVADGSSKFPHGDFNVHAVCETGKLPMSWKPICHLIq--EPFFARYPDGISHFAQECFPEGLSIDRTVRFENDGTMTSHHTYELDDTCVVSRITVNCDGFQPDGPIMRDQLVDILPNETHMFPHGPNAVRQLAFIGFTTADGGLMMGHFDSKMTFNGSRAIEIPGPHFVTIITKQMRDTSDKRDHVCQREVAYAHSVPRIT 229
                                    16        26        36        46        56        |- |      76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226   
                                                                                     65-CRQ                                                                                                                                                                


Chain B from PDB  Type:PROTEIN  Length:221
 aligned with Q2TCH5_9CNID | Q2TCH5 from UniProtKB/TrEMBL  Length:237

    Alignment length:223
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225   
         Q2TCH5_9CNID     6 ALFQSDMTFKIFIDGEVNGQKFTIVADGSSKFPHGDFNVHAVCETGKLPMSWKPICHLIQYGEPFFARYPDGISHFAQECFPEGLSIDRTVRFENDGTMTSHHTYELDDTCVVSRITVNCDGFQPDGPIMRDQLVDILPNETHMFPHGPNAVRQLAFIGFTTADGGLMMGHFDSKMTFNGSRAIEIPGPHFVTIITKQMRDTSDKRDHVCQREVAYAHSVPRI 228
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeeeeeeeee..eeeeeeeeeee.....eeeeeee.........hhhhh....--hhhhh.......hhhhhh....eeeeeeeee....eeeeeeeeeee..eeeeeeeeeee............eeee..eeeeeee....eeeeeeeeeeee....eeeeeeeeeeee...........eeeeeeeeeee.......eeeeeeeeeee..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3a8s B   6 ALFQSDMTFKIFIDGEVNGQKFTIVADGSSKFPHGDFNVHAVCETGKLPMSWKPICHLIq--EPFFARYPDGISHFAQECFPEGLSIDRTVRFENDGTMTSHHTYELDDTCVVSRITVNCDGFQPDGPIMRDQLVDILPNETHMFPHGPNAVRQLAFIGFTTADGGLMMGHFDSKMTFNGSRAIEIPGPHFVTIITKQMRDTSDKRDHVCQREVAYAHSVPRI 228
                                    15        25        35        45        55        65  |     75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225   
                                                                                      65-CRQ
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → 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 3A8S)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3A8S)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3A8S)

(-) Gene Ontology  (2, 2)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (Q2TCH5_9CNID | Q2TCH5)
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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  Cis Peptide Bonds
    Phe A:37 - Pro A:38   [ RasMol ]  
    Phe A:86 - Pro A:87   [ RasMol ]  
    Phe B:37 - Pro B:38   [ RasMol ]  
    Phe B:86 - Pro B:87   [ RasMol ]  
 

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 Related Entries

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

UniProtKB/TrEMBL
        Q2TCH5_9CNID | Q2TCH5: 2wiq 2wis 3gb3 3gl4 3wck 4b30 4zbl 4zfs

(-) Related Entries Specified in the PDB File

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