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(-) Description

Title :  CRYSTAL STRUCTURE OF FULL-LENGTH SPLIT GFP MUTANT D117C DISULFIDE DIMER, P 63 SPACE GROUP
 
Authors :  D. J. Leibly, G. S. Waldo, T. O. Yeates
Date :  20 Aug 14  (Deposition) - 18 Feb 15  (Release) - 27 Jan 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.79
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,C  (1x)
Biol. Unit 2:  B,D  (1x)
Keywords :  Fluorescent Protein, Dimer, Disulfide (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. J. Leibly, M. A. Arbing, I. Pashkov, N. Devore, G. S. Waldo, T. C. Terwilliger, T. O. Yeates
A Suite Of Engineered Gfp Molecules For Oligomeric Scaffolding.
Structure V. 23 1754 2015
PubMed-ID: 26278175  |  Reference-DOI: 10.1016/J.STR.2015.07.008

(-) Compounds

Molecule 1 - FLUORESCENT PROTEIN D117C
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 7)

Asymmetric Unit (2, 7)
No.NameCountTypeFull Name
1ACT3Ligand/IonACETATE ION
2CRO4Mod. Amino Acid{2-[(1R,2R)-1-AMINO-2-HYDROXYPROPYL]-4-(4-HYDROXYBENZYLIDENE)-5-OXO-4,5-DIHYDRO-1H-IMIDAZOL-1-YL}ACETIC ACID
Biological Unit 1 (2, 4)
No.NameCountTypeFull Name
1ACT2Ligand/IonACETATE ION
2CRO2Mod. Amino Acid{2-[(1R,2R)-1-AMINO-2-HYDROXYPROPYL]-4-(4-HYDROXYBENZYLIDENE)-5-OXO-4,5-DIHYDRO-1H-IMIDAZOL-1-YL}ACETIC ACID
Biological Unit 2 (2, 3)
No.NameCountTypeFull Name
1ACT1Ligand/IonACETATE ION
2CRO2Mod. Amino Acid{2-[(1R,2R)-1-AMINO-2-HYDROXYPROPYL]-4-(4-HYDROXYBENZYLIDENE)-5-OXO-4,5-DIHYDRO-1H-IMIDAZOL-1-YL}ACETIC ACID

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPRO A:56 , TRP A:57binding site for residue ACT A 301
2AC2SOFTWAREPRO B:56 , TRP B:57 , HIS B:139binding site for residue ACT B 301
3AC3SOFTWAREPRO C:56 , TRP C:57 , HIS C:139 , TYR C:143binding site for residue ACT C 301

(-) SS Bonds  (2, 2)

Asymmetric Unit
No.Residues
1A:117 -C:117
2B:117 -D:117

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Met A:88 -Pro A:89
2Met B:88 -Pro B:89
3Met C:88 -Pro C:89
4Met D:88 -Pro D:89

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4W6M)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4W6M)

(-) Exons   (0, 0)

(no "Exon" information available for 4W6M)

(-) 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:222
                                                                                                                                                                                                                                                              
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author hhhhhh..eeeeeeeeeee..eeeeeeeeeeee....eeeeeeee........hhhhhh...hhhhh..hhhhhhhhhhhhh....eeeeeeeee....eeeeeeeeeee..eeeeeeeeeee...................eeeeeeee....eeeeeeeeeee.....eeeeeeeeeeee.........eeeeeeeeee........eeeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4w6m A   4 GEELFTGVVPILIELDGDVNGHKFFVRGEGEGDATIGKLSLKFIATTGKLPVPWPTLVTTLxVQAFSRYPDHMKRHDFFKSAMPEGYVQERTIYFKDDGTYKTRAEVKFEGCTLVNRIELKGIDFKEDGNILGHKLEYNFNSHKVYITADKQNNGIKANFTIRHNVEDGSVQLADHYQQNTPIGDGPLPDDHYLSTQTILSKDLNEKRDHMVLLEYVTAAGI 229
                                    13        23        33        43        53        63|||     75        85        95       105       115       125       135       145       155       165       175       185      |197       207       217       227  
                                                                                       64||                                                                                                                         192|                                  
                                                                                        66-CRO                                                                                                                       195                                  
                                                                                         68                                                                                                                                                               


Chain B from PDB  Type:PROTEIN  Length:222
                                                                                                                                                                                                                                                              
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author hhhhh...eeeeeeeeeee..eeeeeeeeeee.....eeeeeeee.......hhhhh.....hhhhh..hhhhhhhhhhhhh....eeeeeeeee....eeeeeeeeeee..eeeeeeeeeee...................eeeeeeee....eeeeeeeeeee.....eeeeeeeeeeee.........eeeeeeeeee........eeeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4w6m B   4 GEELFTGVVPILIELDGDVNGHKFFVRGEGEGDATIGKLSLKFIATTGKLPVPWPTLVTTLxVQAFSRYPDHMKRHDFFKSAMPEGYVQERTIYFKDDGTYKTRAEVKFEGCTLVNRIELKGIDFKEDGNILGHKLEYNFNSHKVYITADKQNNGIKANFTIRHNVEDGSVQLADHYQQNTPIGDGPLPDDHYLSTQTILSKDLNEKRDHMVLLEYVTAAGI 229
                                    13        23        33        43        53        63|||     75        85        95       105       115       125       135       145       155       165       175       185      |197       207       217       227  
                                                                                       64||                                                                                                                         192|                                  
                                                                                        66-CRO                                                                                                                       195                                  
                                                                                         68                                                                                                                                                               


Chain C from PDB  Type:PROTEIN  Length:215
                                                                                                                                                                                                                                                       
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhh...eeeeeeeeeee..eeeeeeeeeee.....eeeeeeee.......hhhhh.....hhhhh..hhhhh..hhhhhh....eeeeeeeee....eeeeeeeeeee..eeeeeeeeeee...................eeeeeeee....eeeeeeeeeee.....eeeeeeeeeeee.....eeeeeeeeee........eeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4w6m C   4 GEELFTGVVPILIELDGDVNGHKFFVRGEGEGDATIGKLSLKFIATTGKLPVPWPTLVTTLxVQAFSRYPDHMKRHDFFKSAMPEGYVQERTIYFKDDGTYKTRAEVKFEGCTLVNRIELKGIDFKEDGNILGHKLEYNFNSHKVYITADKQNNGIKANFTIRHNVEDGSVQLADHYQQNTPIGPDDHYLSTQTILSKDLNEKRDHMVLLEYVTA 226
                                    13        23        33        43        53        63|||     75        85        95       105       115       125       135       145       155       165       175       185   ||  201       211       221     
                                                                                       64||                                                                                                                      189|                              
                                                                                        66-CRO                                                                                                                    196                              
                                                                                         68                                                                                                                                                        


Chain D from PDB  Type:PROTEIN  Length:183
                                                                                                                                                                                                                       
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeeeeee..eeeeeeeeeee.....eeeee.....hhhhh.....hhhhh..hhhhh...eeeeeeeee....eeeeeeeeeee..eeeeeeeeeee............................eeeeeeeeee.....eeeeeeeeeee..eeeeee........eeeeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4w6m D   9 TGVVPILIELDGDVNGHKFFVRGEGEGDATLSLKFIATTLPVPWPTLVTTLxVQAFSRFFKSAMPEGYVQERTIYFKDDGTYKTRAEVKFEGCTLVNRIELKGIDFKEDGNILGHKLEYNFNSHKVTADKQGIKANFTIRHNVEDGSVQLADHYQQNTPSTQTILSKDLNEKRDHMVLLEYVT 225
                                    18        28        38|       53        63|||    |84        94       104       114       124       134       144     ||156||     168       178       202       212       222   
                                                        38|      50|         64||   73|                                                                150| 157|                        187|                       
                                                         42       53          66-CRO 83                                                                 153  160                         202                       
                                                                               68
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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  (0, 0)

(no "SCOP Domain" information available for 4W6M)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4W6M)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4W6M)

(-) Gene Ontology  (0, 0)

Asymmetric Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 4W6M)

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 Related Entries

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(-) Related Entries Specified in the PDB File

4w69 4w6a 4w6b 4w6c 4w6d 4w6f 4w6g 4w6h 4w6i 4w6j 4w6k 4w6l 4w6n 4w6o 4w6p 4w6r 4w6s 4w6t 4w6u 4w72 4w73 4w74 4w75 4w76 4w77 4w7a 4w7c 4w7d 4w7e 4w7f 4w7r