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(-) Description

Title :  CRYSTAL STRUCTURE OF FLUORESCENT PROTEIN UNAG N57A MUTANT
 
Authors :  A. Kumagai, R. Ando, H. Miyatake, A. Miyawaki
Date :  26 Nov 12  (Deposition) - 19 Jun 13  (Release) - 04 Feb 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Biol. Unit 4:  D  (1x)
Keywords :  Fluorescent Protein, Bilirubin Binding Protein, Lipocalin, Beta Barrel, Cytosol (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Kumagai, R. Ando, H. Miyatake, P. Greimel, T. Kobayashi, Y. Hirabayashi, T. Shimogori, A. Miyawaki
A Bilirubin-Inducible Fluorescent Protein From Eel Muscle
Cell(Cambridge, Mass. ) V. 153 1602 2013
PubMed-ID: 23768684  |  Reference-DOI: 10.1016/J.CELL.2013.05.038

(-) Compounds

Molecule 1 - BILIRUBIN-INDUCIBLE FLUORESCENT PROTEIN UNAG
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PGEX-2T
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Mutation: YES
    Organism Common: JAPANESE EEL
    Organism Scientific: ANGUILLA JAPONICA
    Organism Taxid: 7937
    Synonym: UNAGI GREEN FLUORESCENT PROTEIN, UNAG

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): A   
Biological Unit 2 (1x):  B  
Biological Unit 3 (1x):   C 
Biological Unit 4 (1x):    D

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 4)

Asymmetric Unit (1, 4)
No.NameCountTypeFull Name
1BLR4Ligand/Ion3-[5-[(Z)-(4-ETHENYL-3-METHYL-5-OXIDANYLIDENE-PYRROL-2-YLIDENE)METHYL]-2-[[5-[(Z)-(3-ETHENYL-4-METHYL-5-OXIDANYLIDENE-PYRROL-2-YLIDENE)METHYL]-3-(3-HYDROXY-3-OXOPROPYL)-4-METHYL-1H-PYRROL-2-YL]METHYL]-4-METHYL-1H-PYRROL-3-YL]PROPANOIC ACID
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1BLR1Ligand/Ion3-[5-[(Z)-(4-ETHENYL-3-METHYL-5-OXIDANYLIDENE-PYRROL-2-YLIDENE)METHYL]-2-[[5-[(Z)-(3-ETHENYL-4-METHYL-5-OXIDANYLIDENE-PYRROL-2-YLIDENE)METHYL]-3-(3-HYDROXY-3-OXOPROPYL)-4-METHYL-1H-PYRROL-2-YL]METHYL]-4-METHYL-1H-PYRROL-3-YL]PROPANOIC ACID
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1BLR1Ligand/Ion3-[5-[(Z)-(4-ETHENYL-3-METHYL-5-OXIDANYLIDENE-PYRROL-2-YLIDENE)METHYL]-2-[[5-[(Z)-(3-ETHENYL-4-METHYL-5-OXIDANYLIDENE-PYRROL-2-YLIDENE)METHYL]-3-(3-HYDROXY-3-OXOPROPYL)-4-METHYL-1H-PYRROL-2-YL]METHYL]-4-METHYL-1H-PYRROL-3-YL]PROPANOIC ACID
Biological Unit 3 (1, 1)
No.NameCountTypeFull Name
1BLR1Ligand/Ion3-[5-[(Z)-(4-ETHENYL-3-METHYL-5-OXIDANYLIDENE-PYRROL-2-YLIDENE)METHYL]-2-[[5-[(Z)-(3-ETHENYL-4-METHYL-5-OXIDANYLIDENE-PYRROL-2-YLIDENE)METHYL]-3-(3-HYDROXY-3-OXOPROPYL)-4-METHYL-1H-PYRROL-2-YL]METHYL]-4-METHYL-1H-PYRROL-3-YL]PROPANOIC ACID
Biological Unit 4 (1, 1)
No.NameCountTypeFull Name
1BLR1Ligand/Ion3-[5-[(Z)-(4-ETHENYL-3-METHYL-5-OXIDANYLIDENE-PYRROL-2-YLIDENE)METHYL]-2-[[5-[(Z)-(3-ETHENYL-4-METHYL-5-OXIDANYLIDENE-PYRROL-2-YLIDENE)METHYL]-3-(3-HYDROXY-3-OXOPROPYL)-4-METHYL-1H-PYRROL-2-YL]METHYL]-4-METHYL-1H-PYRROL-3-YL]PROPANOIC ACID

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELEU A:21 , THR A:37 , LEU A:41 , ILE A:55 , THR A:65 , PRO A:79 , SER A:80 , LEU A:97 , ARG A:112 , LEU A:119 , ARG A:132 , TYR A:134 , HOH A:301 , HOH A:304 , HOH A:313 , HOH A:316 , HOH A:352BINDING SITE FOR RESIDUE BLR A 200
2AC2SOFTWAREPHE B:17 , LEU B:30 , THR B:37 , LEU B:41 , ILE B:43 , ILE B:55 , VAL B:67 , PRO B:79 , SER B:80 , ARG B:112 , LEU B:119 , TYR B:134 , HOH B:304 , HOH B:306 , HOH B:308 , HOH B:328 , HOH B:329 , HOH B:339BINDING SITE FOR RESIDUE BLR B 200
3AC3SOFTWAREPHE C:17 , LEU C:21 , LEU C:41 , ILE C:43 , MET C:51 , ILE C:55 , ALA C:57 , VAL C:67 , PRO C:79 , SER C:80 , ARG C:112 , LEU C:119 , ARG C:132 , TYR C:134 , HOH C:306 , HOH C:325BINDING SITE FOR RESIDUE BLR C 200
4AC4SOFTWAREPHE D:17 , LEU D:21 , LEU D:30 , LEU D:41 , ILE D:43 , MET D:51 , VAL D:53 , ILE D:55 , ALA D:57 , VAL D:67 , PRO D:79 , SER D:80 , ARG D:112 , LEU D:119 , ARG D:132 , TYR D:134 , HOH D:316 , HOH D:328 , HOH D:372 , HOH D:406 , HOH D:407BINDING SITE FOR RESIDUE BLR D 200

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4I3D)

(-) Cis Peptide Bonds  (6, 6)

Asymmetric Unit
No.Residues
1Pro A:59 -Pro A:60
2Ala A:137 -Thr A:138
3Pro B:59 -Pro B:60
4Pro C:59 -Pro C:60
5Thr C:138 -Glu C:139
6Pro D:59 -Pro D:60

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4I3D)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4I3D)

(-) Exons   (0, 0)

(no "Exon" information available for 4I3D)

(-) Sequences/Alignments

Asymmetric 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:139
                                                                                                                                                                           
               SCOP domains d4i3da_ A: automated matches                                                                                                                SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhheeeeeeeeehhhhhhhhh..hhhhhhhhhhh..eeeeeee...eeeeeee........eeeeee....ee..........eeeeeee..eeeeeeee..eeeeeeeeee..eeeeeeee..eeeeeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4i3d A   1 MVEKFVGTWKIADSHNFGEYLKAIGAPKELSDGGDATTPTLYISQKDGDKMTVKIEAGPPTFLDTQVKFKLGEEFDEFPSDRRKGVKSVVNLVGEKLVYVQKWDGKETTYVREIKDGKLVVTLTMGDVVAVRSYRRATE 139
                                    10        20        30        40        50        60        70        80        90       100       110       120       130         


Chain B from PDB  Type:PROTEIN  Length:139
                                                                                                                                                                           
               SCOP domains d4i3db_ B: automated matches                                                                                                                SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhh.eeeeeeeeehhhhhhhhh..hhhhhh.......eeeeee....eeeeeee........eeeeee....eee........eeeeeeee..eeeeeeee..eeeeeeeeee..eeeeeeee..eeeeeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4i3d B   1 MVEKFVGTWKIADSHNFGEYLKAIGAPKELSDGGDATTPTLYISQKDGDKMTVKIEAGPPTFLDTQVKFKLGEEFDEFPSDRRKGVKSVVNLVGEKLVYVQKWDGKETTYVREIKDGKLVVTLTMGDVVAVRSYRRATE 139
                                    10        20        30        40        50        60        70        80        90       100       110       120       130         


Chain C from PDB  Type:PROTEIN  Length:139
                                                                                                                                                                           
               SCOP domains d4i3dc_ C: automated matches                                                                                                                SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhh.eeeeeeeeehhhhhhhhh..hhhhhhhhhhh..eeeeeee...eeeeeee........eeeeee....ee..........eeeeeee..eeeeeeee..eeeeeeeeee..eeeeeeee..eeeeeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4i3d C   1 MVEKFVGTWKIADSHNFGEYLKAIGAPKELSDGGDATTPTLYISQKDGDKMTVKIEAGPPTFLDTQVKFKLGEEFDEFPSDRRKGVKSVVNLVGEKLVYVQKWDGKETTYVREIKDGKLVVTLTMGDVVAVRSYRRATE 139
                                    10        20        30        40        50        60        70        80        90       100       110       120       130         


Chain D from PDB  Type:PROTEIN  Length:139
                                                                                                                                                                           
               SCOP domains d4i3dd_ D: automated matches                                                                                                                SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhheeeeeeeeehhhhhhhhh..hhhhhhhhhhh..eeeeeee...eeeeeee.......eeeeeee....ee..........eeeeeee..eeeeeeee..eeeeeeeeee..eeeeeeee..eeeeeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4i3d D   1 MVEKFVGTWKIADSHNFGEYLKAIGAPKELSDGGDATTPTLYISQKDGDKMTVKIEAGPPTFLDTQVKFKLGEEFDEFPSDRRKGVKSVVNLVGEKLVYVQKWDGKETTYVREIKDGKLVVTLTMGDVVAVRSYRRATE 139
                                    10        20        30        40        50        60        70        80        90       100       110       120       130
   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  (1, 4)

Asymmetric Unit
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4I3D)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4I3D)

(-) Gene Ontology  (5, 8)

Asymmetric Unit(hide GO term definitions)

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 Related Entries

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

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        UNAG_ANGJA | P0DM59: 4i3b 4i3c

(-) Related Entries Specified in the PDB File

4i3b 4i3c