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(-) Description

Title :  CRYSTAL STRUCTURE OF THE YELLOW FLUORESCENT PROTEIN PHIYFP (PHIALIDIUM SP.)
 
Authors :  N. Pletneva, S. Pletnev, V. Z. Pletnev
Date :  03 Oct 12  (Deposition) - 29 May 13  (Release) - 19 Jun 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.05
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Phiyfp, Yellow Fluorescent Protein, Mutant Variant Of Phiyfp, Thr- Tyr-Gly Chromophore, Beta-Barrel, Biomarker, Thr-Tyr-Gly Bicyclic Chromophore, Fluorescent Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  N. V. Pletneva, V. Z. Pletnev, E. Souslova, D. M. Chudakov, S. Lukyanov V. I. Martynov, S. Arhipova, I. Artemyev, A. Wlodawer, Z. Dauter, S. Pletnev
Yellow Fluorescent Protein Phiyfpv (Phialidium): Structure And Structure-Based Mutagenesis.
Acta Crystallogr. , Sect. D V. 69 1005 2013
PubMed-ID: 23695245  |  Reference-DOI: 10.1107/S0907444913004034

(-) Compounds

Molecule 1 - YELLOW FLUORESCENT PROTEIN
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PQE30
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Organism Scientific: PHIALIDIUM SP. SL-2003
    Organism Taxid: 258839

 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
1CRO2Mod. Amino Acid{2-[(1R,2R)-1-AMINO-2-HYDROXYPROPYL]-4-(4-HYDROXYBENZYLIDENE)-5-OXO-4,5-DIHYDRO-1H-IMIDAZOL-1-YL}ACETIC ACID

(-) Sites  (0, 0)

(no "Site" information available for 4HE4)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4HE4)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Met A:86 -Pro A:87
2Met B:86 -Pro B:87

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4HE4)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4HE4)

(-) Exons   (0, 0)

(no "Exon" information available for 4HE4)

(-) 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:232
                                                                                                                                                                                                                                                                        
               SCOP domains d4he4a_ A: automated matches                                                                                                                                                                                                             SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhh..eeeeeeeeeee..eeeeeeeeeeee....eeeeeeee.......hhhhhh....hhhhh.......hhhhhh....eeeeeeeee....eeeeeeeeeee..eeeeeeeeeee...................eeeeeeeehhhheeeeeeeeeee.......eeeeeeeeeeee...........eeeeeeeeee........eeeeeeeeeeehhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4he4 A   1 GSSGALLFHGKIPYVVEMEGNVDGHTFSIRGKGYGDASVGKVDAQFICTTGDVPVPWSTLVTTLgAQCFAKYGPELKDFYKSCMPDGYVQERTITFEGDGNFKTRAEVTFENGSVYNRVKLNGQGFKKDGHVLGKNLEFNFTPHCLYIWGDQANHGLKSAFKICHEITGSKGDFIVADHTQMNTPIGGGPVHVPEYHHMSYHVKLSKDVTDHRDNMSLKETVRAVDCRKTYD 234
                                    10        20        30        40        50        60    ||  72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232  
                                                                                           65-CRO                                                                                                                                                                   
                                                                                            68                                                                                                                                                                      


Chain B from PDB  Type:PROTEIN  Length:232
                                                                                                                                                                                                                                                                        
               SCOP domains d4he4b_ B: automated matches                                                                                                                                                                                                             SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhh..eeeeeeeeeee..eeeeeeeeeeee....eeeeeeee.......hhhhhh....hhhhh.......hhhhhh....eeeeeeeee....eeeeeeeeeee..eeeeeeeeeee...................eeeeeeeehhhheeeeeeeeeee.......eeeeeeeeeeee...........eeeeeeeeee........eeeeeeeeeeehhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4he4 B   1 GSSGALLFHGKIPYVVEMEGNVDGHTFSIRGKGYGDASVGKVDAQFICTTGDVPVPWSTLVTTLgAQCFAKYGPELKDFYKSCMPDGYVQERTITFEGDGNFKTRAEVTFENGSVYNRVKLNGQGFKKDGHVLGKNLEFNFTPHCLYIWGDQANHGLKSAFKICHEITGSKGDFIVADHTQMNTPIGGGPVHVPEYHHMSYHVKLSKDVTDHRDNMSLKETVRAVDCRKTYD 234
                                    10        20        30        40        50        60    ||  72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232  
                                                                                           65-CRO                                                                                                                                                                   
                                                                                            68
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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 4HE4)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4HE4)

(-) Gene Ontology  (2, 2)

Asymmetric/Biological Unit(hide GO term definitions)

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(-) Related Entries Specified in the PDB File

2ogr CRYSTAL STRUCTURE OF YELLOW FLUORESCENT PROTEIN FROM ZOANTHUS SP. AT 1.8A RESOLUTION