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(-) Description

Title :  CRYSTAL STRUCTURE OF GREEN FLUORESCENT PROTEIN LANGFP(BRANCHIOSTOMA LANCEOLATUM)
 
Authors :  Pletnev V. Z. , Pletneva N. V. , Pletnev S. V.
Date :  06 Nov 12  (Deposition) - 18 Sep 13  (Release) - 18 Sep 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.70
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Langfp, Green Fluorescent Protein, Beta-Barrel, Gly-Tyr-Gly Chromophore, Biomarker, Cephalochordate, Fluorescent Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  V. Z. Pletnev, N. V. Pletneva, K. A. Lukyanov, E. A. Souslova, A. F. Fradkov, D. M. Chudakov, T. Chepurnykh, I. V. Yampolsky, A. Wlodawer, Z. Dauter, S. Pletnev
Structure Of The Red Fluorescent Protein From A Lancelet (Branchiostoma Lanceolatum): A Novel Gyg Chromophore Covalently Bound To A Nearby Tyrosine.
Acta Crystallogr. , Sect. D V. 69 1850 2013
PubMed-ID: 23999308  |  Reference-DOI: 10.1107/S0907444913015424

(-) Compounds

Molecule 1 - GREEN FLUORESCENT PROTEIN BLFP-Y6
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PQE30
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: N-TERMINAL
    Gene: BLFP-Y6
    Mutation: YES
    Organism Common: COMMON LANCELET
    Organism Scientific: BRANCHIOSTOMA LANCEOLATUM
    Organism Taxid: 7740

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 6)

Asymmetric/Biological Unit (2, 6)
No.NameCountTypeFull Name
1CR24Mod. Amino Acid{(4Z)-2-(AMINOMETHYL)-4-[(4-HYDROXYPHENYL)METHYLIDENE]-5-OXO-4,5-DIHYDRO-1H-IMIDAZOL-1-YL}ACETIC ACID
2GOL2Ligand/IonGLYCEROL

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:8 , LEU A:9 , VAL A:23 , GLY A:24 , ARG A:25 , HOH A:337 , ASN C:208 , HOH C:528BINDING SITE FOR RESIDUE GOL C 301
2AC2SOFTWARELYS C:197 , TRP C:212BINDING SITE FOR RESIDUE GOL C 302

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (8, 8)

Asymmetric/Biological Unit
No.Residues
1Val A:54 -Pro A:55
2Gln A:190 -Pro A:191
3Val B:54 -Pro B:55
4Gln B:190 -Pro B:191
5Val C:54 -Pro C:55
6Gln C:190 -Pro C:191
7Val D:54 -Pro D:55
8Gln D:190 -Pro D:191

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4HVF)

(-) 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:218
                                                                                                                                                                                                                                                          
               SCOP domains d4hvfa_ A: automated matches                                                                                                                                                                                               SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeeeeeeee..eeeeeeeeeeee....eeeeeeee.......hhhhhh....hhhhh.hhhhh.hhhhhhhhh...eeeeeeeee....eeeeeeeeeee..eeeeeeeeeee............eeee..eeeeeeeee..eeeeeeeeeeee.....eeeeeeeeeee....hhhhhh...eeeeeeeeeee...eeeeeeeeeee.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4hvf A   1 SLLPATHELHIFGSINSLEFDLVGRGTGNPKEGYEELHLKSTKSALQFSPWILVPQIgFYQYLPFPDGAMSPFQAAMNDGSGYQVHRTMQFEDGATLTGIYRYTYEGTHIKGEFQVIGTGFPADGPVMTNSLTAADWCVTKIVYPNENTIIDKFDWTYTTTSGKRYQSNVRSNFTFAKPIAANILQKQPMFVFRKTELKHSKTELNFKEWQTAFSDVM 220
                                    10        20        30        40        50       |62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212        
                                                                                    58-CR2                                                                                                                                                            
                                                                                     61                                                                                                                                                               


Chain B from PDB  Type:PROTEIN  Length:218
                                                                                                                                                                                                                                                          
               SCOP domains d4hvfb_ B: automated matches                                                                                                                                                                                               SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeeeeeeee..eeeeeeeeeeee....eeeeeeee.......hhhhhh....hhhh.eehhheehhhhhhhhh...eeeeeeeee....eeeeeeeeeee..eeeeeeeeeee............eeee..eeeeeeeee..eeeeeeeeeeee.....eeeeeeeeeee....hhhhhh...eeeeeeeeeee...eeeeeeeeeee.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4hvf B   1 SLLPATHELHIFGSINSLEFDLVGRGTGNPKEGYEELHLKSTKSALQFSPWILVPQIgFYQYLPFPDGAMSPFQAAMNDGSGYQVHRTMQFEDGATLTGIYRYTYEGTHIKGEFQVIGTGFPADGPVMTNSLTAADWCVTKIVYPNENTIIDKFDWTYTTTSGKRYQSNVRSNFTFAKPIAANILQKQPMFVFRKTELKHSKTELNFKEWQTAFSDVM 220
                                    10        20        30        40        50       |62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212        
                                                                                    58-CR2                                                                                                                                                            
                                                                                     61                                                                                                                                                               


Chain C from PDB  Type:PROTEIN  Length:218
                                                                                                                                                                                                                                                          
               SCOP domains d4hvfc_ C: automated matches                                                                                                                                                                                               SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeeeeeeee..eeeeeeeeeeee....eeeeeeee.......hhhhhh....hhhhh.hhhhh.hhhhhhhhh...eeeeeeeee....eeeeeeeeeee..eeeeeeeeeee............eeee..eeeeeeeee..eeeeeeeeeeee.....eeeeeeeeeee....hhhhhh...eeeeeeeeeee...eeeeeeeeeee.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4hvf C   1 SLLPATHELHIFGSINSLEFDLVGRGTGNPKEGYEELHLKSTKSALQFSPWILVPQIgFYQYLPFPDGAMSPFQAAMNDGSGYQVHRTMQFEDGATLTGIYRYTYEGTHIKGEFQVIGTGFPADGPVMTNSLTAADWCVTKIVYPNENTIIDKFDWTYTTTSGKRYQSNVRSNFTFAKPIAANILQKQPMFVFRKTELKHSKTELNFKEWQTAFSDVM 220
                                    10        20        30        40        50       |62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212        
                                                                                    58-CR2                                                                                                                                                            
                                                                                     61                                                                                                                                                               


Chain D from PDB  Type:PROTEIN  Length:225
                                                                                                                                                                                                                                                                 
               SCOP domains d4hvfd_ D: automated matches                                                                                                                                                                                                      SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ............eeeeeeeeee..eeeeeeeeeeee....eeeeeeee.......hhhhhh....hhhhh.hhhhh.hhhhhhhhh...eeeeeeeee....eeeeeeeeeee..eeeeeeeeeee............eeee..eeeeeeeee..eeeeeeeeeeee....eeeeeeeeeeee....hhhhhh...eeeeeeeeeee...eeeeeeeeeee.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4hvf D  -6 HHHHHHGSLLPATHELHIFGSINSLEFDLVGRGTGNPKEGYEELHLKSTKSALQFSPWILVPQIgFYQYLPFPDGAMSPFQAAMNDGSGYQVHRTMQFEDGATLTGIYRYTYEGTHIKGEFQVIGTGFPADGPVMTNSLTAADWCVTKIVYPNENTIIDKFDWTYTTTSGKRYQSNVRSNFTFAKPIAANILQKQPMFVFRKTELKHSKTELNFKEWQTAFSDVM 220
                                     3        13        23        33        43        53    ||  65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215     
                                                                                           58-CR2                                                                                                                                                            
                                                                                            61
   Legend:   → Mismatch (orange background)
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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, 4)

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

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (1, 2)

Asymmetric/Biological Unit(hide GO term definitions)

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 Related Entries

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(-) Related Entries Specified in the PDB File

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