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(-) Description

Title :  CRYSTAL STRUCTURE OF THE ENGINEERED FLUORESCENT PROTEIN MRUBY, CRYSTAL FORM 1, PH 4.5
 
Authors :  J. Akerboom, L. L. Looger, E. R. Schreiter
Date :  28 Sep 11  (Deposition) - 03 Oct 12  (Release) - 29 Jan 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.25
Chains :  Asym./Biol. Unit :  A
Keywords :  Fluorescent Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Akerboom, N. Carreras Calderon, L. Tian, S. Wabnig, M. Prigge, J. Tolo, A. Gordus, M. B. Orger, K. E. Severi, J. J. Macklin, R. Patel, S. R. Pulver, T. J. Wardill, E. Fischer, C. Schuler, T. W. Chen, K. S. Sarkisyan, J. S. Marvin, C. I. Bargmann, D. S. Kim, S. Kugler, L. Lagnado, P. Hegemann, A. Gottschalk, E. R. Schreiter, L. L. Looger
Genetically Encoded Calcium Indicators For Multi-Color Neural Activity Imaging And Combination With Optogenetics.
Front Mol Neurosci V. 6 2 2013
PubMed-ID: 23459413  |  Reference-DOI: 10.3389/FNMOL.2013.00002

(-) Compounds

Molecule 1 - MRUBY
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Mutation: YES
    Organism Common: BUBBLE-TIP ANEMONE
    Organism Scientific: ENTACMAEA QUADRICOLOR
    Organism Taxid: 6118
    Synonym: GFP-LIKE CHROMOPROTEIN

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (2, 2)
No.NameCountTypeFull Name
1ACT1Ligand/IonACETATE ION
2NRQ1Mod. Amino Acid{(4Z)-4-(4-HYDROXYBENZYLIDENE)-2-[3-(METHYLTHIO)PROPANIMIDOYL]-5-OXO-4,5-DIHYDRO-1H-IMIDAZOL-1-YL}ACETIC ACID

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLN A:39 , NRQ A:64 , SER A:66 , ARG A:67 , ILE A:70 , GLU A:215 , ALA A:217BINDING SITE FOR RESIDUE ACT A 228

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3U0L)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Gly A:49 -Pro A:50
2Phe A:84 -Pro A:85

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3U0L)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3U0L)

(-) Exons   (0, 0)

(no "Exon" information available for 3U0L)

(-) 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:217
 aligned with RFP_ENTQU | Q8ISF8 from UniProtKB/Swiss-Prot  Length:231

    Alignment length:219
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212         
            RFP_ENTQU     3 SLIKENMRMMVVMEGSVNGYQFKCTGEGDGNPYMGTQTMRIKVVEGGPLPFAFDILATSFMYGSKTFIKHTKGIPDFFKQSFPEGFTWERVTRYEDGGVFTVMQDTSLEDGCLVYHAKVTGVNFPSNGAVMQKKTKGWEPNTEMLYPADGGLRGYSQMALNVDGGGYLSCSFETTYRSKKTVENFKMPGFHFVDHRLERLEESDKEMFVVQHEHAVAKF 221
               SCOP domains d3u0la_ A: 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...eeeeeeeeeeeee............eeeeeeeeeeee.....eeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3u0l A   3 SLIKENMRMKVVLEGSVNGHQFKCTGEGEGNPYMGTQTMRIKVIEGGPLPFAFDILATSF-m-SRTFIKYPKGIPDFFKQSFPEGFTWERVTRYEDGGVITVMQDTSLEDGCLVYHAQVRGVNFPSNGAVMQKKTKGWEPNTEMMYPADGGLRGYTHMALKVDGGGHLSCSFVTTYRSKKTVGNIKMPGIHAVSHRLERLEESDNEMFVVQREHAVAKF 221
                                    12        22        32        42        52        62 | |    72        82        92       102       112       122       132       142       152       162       172       182       192       202       212         
                                                                                      62 | |                                                                                                                                                           
                                                                                        64-NRQ                                                                                                                                                         
                                                                                          66
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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, 1)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3U0L)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3U0L)

(-) Gene Ontology  (2, 2)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (RFP_ENTQU | Q8ISF8)
biological process
    GO:0008218    bioluminescence    The production of light by certain enzyme-catalyzed reactions in cells.
    GO:0018298    protein-chromophore linkage    The covalent or noncovalent attachment of a chromophore to a protein.

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 Related Entries

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

UniProtKB/Swiss-Prot
        RFP_ENTQU | Q8ISF8: 1uis 3e5t 3e5v 3e5w 3ip2 3u0m 3u0n

(-) Related Entries Specified in the PDB File

3u0m 3u0n