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(-) Description

Title :  CRYSTAL STRUCTURE OF FULL-LENGTH SPLIT GFP MUTANT D117C DISULFIDE DIMER, C 1 2 1 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 :  3.38
Chains :  Asym. Unit :  A,B,C,D,E,F
Biol. Unit 1:  A,D  (1x)
Biol. Unit 2:  B,F  (1x)
Biol. Unit 3:  C,E  (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, E, F
    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

  123456
Asymmetric Unit : ABCDEF
Biological Unit 1 (1x): A  D  
Biological Unit 2 (1x):  B   F
Biological Unit 3 (1x):   C E 

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (1, 4)
No.NameCountTypeFull Name
1CRO4Mod. 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 (1, 1)
No.NameCountTypeFull Name
1CRO1Mod. 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 (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
Biological Unit 3 (1, 1)
No.NameCountTypeFull Name
1CRO1Mod. 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 4W6N)

(-) SS Bonds  (3, 3)

Asymmetric Unit
No.Residues
1A:117 -D:117
2B:117 -F:117
3C:117 -E:117

(-) Cis Peptide Bonds  (4, 4)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4W6N)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4W6N)

(-) Exons   (0, 0)

(no "Exon" information available for 4W6N)

(-) 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:217
                                                                                                                                                                                                                                                         
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhh.eeeeeeeeeeee.....eeeeeee....eeeeeee........hhhhhh....hhhhh..hhhhhhhhhhhhh....eeeeeeeee....eeeeeeeeee....eeeeeeeeee...................eeeeeeee....eeee.eeee....eeeeeeeeeeee.........eeeeeeeeee........eeeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4w6n A   4 GEELFTGVVPILIELDGDVNGHKVRGEGEGDATIGKLSLKFIATTGKLPVPWPTLVTTLxVQAFSRYPDHMKRHDFFKSAMPEGYVQERTIYFKDDGTYKTRAEVKFEGCTLVNRIELKGIDFKEDGNILGHKLEYNFNSHKVYITADKQNNGIKATIRHNVDGSVQLADHYQQNTPIGDGPLPDDHYLSTQTILSKDLNEKRDHMVLLEYVTAAGI 229
                                    13        23  ||    35        45        55        66|       77        87        97       107       117       127       137       147       157     ||169 ||    180       190 ||    202       212       222       
                                                 26|                                 64||                                                                                            163|  171|                192|                                  
                                                  29                                  66-CRO                                                                                          166   173                 195                                  
                                                                                       68                                                                                                                                                            


Chain B from PDB  Type:PROTEIN  Length:218
                                                                                                                                                                                                                                                          
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhh..eeeeeeeeeee..eeeeeeeeeee.....eeeeeee.................hhhhh..hhhhhhhhhhhhh...eeeeeeeee....eeeeeeeeeee..eeeeeeeeeee....................eeeeeee....eeeeeeeeeee.....eeeeeeeeeeee.........eeeeeeeeee........eeeeeeeeeee Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4w6n B   4 GEELFTGVVPILIELDGDVNGHKFFVRGEGEGDATIGKLSLKFIATTKLPVPWPTLVTTLxVQAFSRYPDHMKRHDFFKSAPEGYVQERTIYFKDDGTYKTRAEVKFEGCTLVNRIELKGIDFKEDGNILGHKLEYNFNSHKVYITADKQNNGIKANFTIRHNVEDGSVQLADHYQQNTPIGDGPLPDDHYLSTQTILSKDLNEKRDHMVLLEYVTAA 227
                                    13        23        33        43      ||54        64||      76        86||      97       107       117       127       137       147       157       167       177       187    || 199       209       219        
                                                                         50|          64||                 87|                                                                                                    192|                                
                                                                          52           66-CRO               89                                                                                                     195                                
                                                                                        68                                                                                                                                                            


Chain C from PDB  Type:PROTEIN  Length:219
                                                                                                                                                                                                                                                           
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhh.eeeeeeeeeeee..eeeeeeeeeeee....eeeeeee........hhhhhh...hhhhh..hhhhhhhhhhhhh....eeeeeeeee....eeeeeeeeeee..eeeeeeeeeee....................eeeeeee....eeeeeeeeeee.....eeeeeeeeeeee........eeeeeeeeee........eeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4w6n C   4 GEELFTGVVPILIELDGDVNGHKFFVRGEGEGDATIGKLSLKFIATTGKLPVPWPTLVTTxVQAFSRYPDHMKRHDFFKSAMPEGYVQERTIYFKDDGTYKTRAEVKFEGCTLVNRIELKGIDFKEDGNILGHKLEYNFNSHKVYITADKQNNGIKANFTIRHNVEDGSVQLADHYQQNTPIGDGLPDDHYLSTQTILSKDLNEKRDHMVLLEYVTAAG 228
                                    13        23        33        43        53        63||      76        86        96       106       116       126       136       146       156       166       176       186    || 199       209       219         
                                                                                      63||                                                                                                                        191|                                 
                                                                                       66-CRO                                                                                                                      195                                 
                                                                                        68                                                                                                                                                             


Chain D from PDB  Type:PROTEIN  Length:221
                                                                                                                                                                                                                                                             
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhh.eeeeeeeeeeee..eeeeeeeeeeee....eeeeeeee................hhhhh..hhhhhhhhhhhhh....eeeeeeeee....eeeeeeeeee...eeeeeeeeee....................eeeeeee....eeeeeeeeeee.....eeeeeeeeeeee.........eeeeeeeeee........eeeeeeeeeee... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4w6n D   4 GEELFTGVVPILIELDGDVNGHKFFVRGEGEGDATIGKLSLKFIATTGKLPVPWPTLVTTLVQAFSRYPDHMKRHDFFKSAMPEGYVQERTIYFKDDGTYKTRAEVKFECTLVNRIELKGIDFKEDGNILGHKLEYNFNSHKVYITADKQNNGIKANFTIRHNVEDGSVQLADHYQQNTPIGDGPLPDDHYLSTQTILSKDLNEKRDHMVLLEYVTAAGIT 230
                                    13        23        33        43        53        63||      76        86        96       106       117       127       137       147       157       167       177       187    || 199       209       219       229 
                                                                                       64|                                            115|                                                                        192|                                   
                                                                                        68                                             117                                                                         195                                   


Chain E from PDB  Type:PROTEIN  Length:221
                                                                                                                                                                                                                                                             
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhh.eeeeeeeeeeee..eeeeeeeeeeee....eeeeeeee.......hhhhhh...hhhhh..hhhhhhhhhhhhh...eeeeeeeee....eeeeeeeeeee..eeeeeeeeeee....................eeeeeee....eeeeeeeeeee.....eeeeeeeeeeee.........eeeeeeeeee........eeeeeeeeeee... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4w6n E   4 GEELFTGVVPILIELDGDVNGHKFFVRGEGEGDATIGKLSLKFIATTGKLPVPWPTLVTTLVQAFSRYPDHMKRHDFFKSAPEGYVQERTIYFKDDGTYKTRAEVKFEGCTLVNRIELKGIDFKEDGNILGHKLEYNFNSHKVYITADKQNNGIKANFTIRHNVEDGSVQLADHYQQNTPIGDGPLPDDHYLSTQTILSKDLNEKRDHMVLLEYVTAAGIT 230
                                    13        23        33        43        53        63||      76        86||      97       107       117       127       137       147       157       167       177       187    || 199       209       219       229 
                                                                                       64|                 87|                                                                                                    192|                                   
                                                                                        68                  89                                                                                                     195                                   


Chain F from PDB  Type:PROTEIN  Length:210
                                                                                                                                                                                                                                                  
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author hhhhhh..eeeeeeeeeee..eeeeeeeeeee.....eeeeeee..................hhhhh..hhhhhhhh.......eeeeeee....eeeeeeeeeee..eeeeeeeeeee....................eeeeeee...eeeeeeeeeee.....eeeeeeeeee......eeeeeeeeee........eeeeeeeeeee Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4w6n F   4 GEELFTGVVPILIELDGDVNGHKFFVRGEGEGDATIGKLSLKFIATTGKLPVPWPTLVTTLxVQAFSRYPDHMKRHDKSAMPEVQERTIYFKDDGTYKTRAEVKFEGCTLVNRIELKGIDFKEDGNILGHKLEYNFNSHKVYITADKNNGIKANFTIRHNVEDGSVQLADHYQQNTPIGDDHYLSTQTILSKDLNEKRDHMVLLEYVTAA 227
                                    13        23        33        43        53        63|||     75      ||87  ||    99       109       119       129       139       149      |160       170       180       197       207       217       227
                                                                                       64||            82|   90|                                                            156|                            189|                              
                                                                                        66-CRO          85    93                                                             158                             197                              
                                                                                         68
   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  (0, 0)

(no "SCOP Domain" information available for 4W6N)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4W6N)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4W6N)

(-) Gene Ontology  (0, 0)

Asymmetric Unit(hide GO term definitions)
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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 4w6m 4w6o 4w6p 4w6r 4w6s 4w6t 4w6u 4w72 4w73 4w74 4w75 4w76 4w77 4w7a 4w7c 4w7d 4w7e 4w7f 4w7r