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(-) Description

Title :  CRYSTAL STRUCTURE OF RED FLUORESCENT PROTEIN EQFP578 CRYSTALLIZED AT PH 4.0
 
Authors :  S Pletnev, N. V. Pletneva, V. Z. Pletnev
Date :  09 Nov 10  (Deposition) - 25 May 11  (Release) - 27 Mar 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.75
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Eqfp578, Red Fluorescent Protein, Beta-Barrel, Biomarker, Met-Tyr-Gly Chromophore, Fluorescent Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  N. V. Pletneva, V. Z. Pletnev, I. I. Shemiakina, D. M. Chudakov, I. Artemyev, A. Wlodawer, Z. Dauter, S. Pletnev
Crystallographic Study Of Red Fluorescent Protein Eqfp578 And Its Far-Red Variant Katushka Reveals Opposite Ph-Induce Isomerization Of Chromophore.
Protein Sci. V. 20 1265 2011
PubMed-ID: 21563226  |  Reference-DOI: 10.1002/PRO.654

(-) Compounds

Molecule 1 - RED FLUORESCENT PROTEIN EQFP578
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PQE30
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Organism Common: SEA ANEMONES
    Organism Scientific: ENTACMAEA QUADRICOLOR
    Organism Taxid: 6118

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

Asymmetric/Biological Unit (2, 4)
No.NameCountTypeFull Name
1GOL2Ligand/IonGLYCEROL
2NRQ2Mod. Amino Acid{(4Z)-4-(4-HYDROXYBENZYLIDENE)-2-[3-(METHYLTHIO)PROPANIMIDOYL]-5-OXO-4,5-DIHYDRO-1H-IMIDAZOL-1-YL}ACETIC ACID

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPHE A:194 , TYR A:221 , CYS A:222 , ASP A:223 , HOH A:379 , THR B:144 , ASP B:196BINDING SITE FOR RESIDUE GOL A 232
2AC2SOFTWAREHOH B:64 , LYS B:135 , LYS B:207 , HOH B:367BINDING SITE FOR RESIDUE GOL B 232

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (4, 4)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3PJB)

(-) 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:223
 aligned with H3JQU7_ENTQU | H3JQU7 from UniProtKB/TrEMBL  Length:231

    Alignment length:225
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221     
         H3JQU7_ENTQU     2 SELIKENMHMKLYMEGTVNNHHFKCTSEGEGKPYEGTQTMKIKVVEGGPLPFAFDILATSFMYGSKTFINHTQGIPDFFKQSFPEGFTWERITTYEDGGVLTATQDTSLQNGCIIYNVKINGVNFPSNGSVMQKKTLGWEANTEMLYPADGGLRGHSQMALKLVGGGYLHCSFKTTYRSKKPAKNLKMPGFHFVDHRLERIKEADKETYVEQHEMAVAKYCDLPS 226
               SCOP domains d3pjba_ A: automated matches                                                                                                                                                                                                      SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......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
                 3pjb A   2 SELIKENMHMKLYMEGTVNNHHFKCTSEGEGKPYEGTQTMKIKVVEGGPLPFAFDILATSFm--SKTFINHTQGIPDFFKQSFPEGFTWERITTYEDGGVLTATQDTSLQNGCIIYNVKINGVNFPSNGSVMQKKTLGWEANTEMLYPADGGLRGHSQMALKLVGGGYLHCSFKTTYRSKKPAKNLKMPGFHFVDHRLERIKEADKETYVEQHEMAVAKYCDLPS 226
                                    11        21        31        41        51        61 |  |   71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221     
                                                                                        63-NRQ                                                                                                                                                               


Chain B from PDB  Type:PROTEIN  Length:223
 aligned with H3JQU7_ENTQU | H3JQU7 from UniProtKB/TrEMBL  Length:231

    Alignment length:225
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221     
         H3JQU7_ENTQU     2 SELIKENMHMKLYMEGTVNNHHFKCTSEGEGKPYEGTQTMKIKVVEGGPLPFAFDILATSFMYGSKTFINHTQGIPDFFKQSFPEGFTWERITTYEDGGVLTATQDTSLQNGCIIYNVKINGVNFPSNGSVMQKKTLGWEANTEMLYPADGGLRGHSQMALKLVGGGYLHCSFKTTYRSKKPAKNLKMPGFHFVDHRLERIKEADKETYVEQHEMAVAKYCDLPS 226
               SCOP domains d3pjbb_ B: automated matches                                                                                                                                                                                                      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
                 3pjb B   2 SELIKENMHMKLYMEGTVNNHHFKCTSEGEGKPYEGTQTMKIKVVEGGPLPFAFDILATSFm--SKTFINHTQGIPDFFKQSFPEGFTWERITTYEDGGVLTATQDTSLQNGCIIYNVKINGVNFPSNGSVMQKKTLGWEANTEMLYPADGGLRGHSQMALKLVGGGYLHCSFKTTYRSKKPAKNLKMPGFHFVDHRLERIKEADKETYVEQHEMAVAKYCDLPS 226
                                    11        21        31        41        51        61 |  |   71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221     
                                                                                        63-NRQ
   Legend:   → Mismatch (orange background)
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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  (1, 2)

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

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (1, 1)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (H3JQU7_ENTQU | H3JQU7)
biological process
    GO:0008218    bioluminescence    The production of light by certain enzyme-catalyzed reactions in cells.

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 Related Entries

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

(no "Entries Sharing at Least One Protein Chain" available for 3PJB)

(-) Related Entries Specified in the PDB File

3bx9 MONOMERIC FAR-RED FLUORESCENT PROTEIN MKATE CRYSTALLIZED AT PH 2.0
3bxa MONOMERIC FAR-RED FLUORESCENT PROTEIN MKATE CRYSTALLIZED AT PH 4.2
3bxb MONOMERIC FAR-RED FLUORESCENT PROTEIN MKATE CRYSTALLIZED AT PH 7.0
3bxc MONOMERIC FAR-RED FLUORESCENT PROTEIN MKATE CRYSTALLIZED AT PH 9.0
3pib FAR-RED FLUORESCENT PROTEIN EQFP578 CRYSTALLIZED AT PH 5.5
3pj5 FAR-RED FLUORESCENT PROTEIN KATUSHKA CRYSTALLIZED AT PH 5.0
3pj7 FAR-RED FLUORESCENT PROTEIN KATUSHKA CRYSTALLIZED AT PH 8.5