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(-) Description

Title :  CRYSTAL STRUCTURE OF FULL-LENGTH SPLIT GFP MUTANT D21H/K26C DISULFIDE AND METAL-MEDIATED DIMER, P 21 21 21 SPACE GROUP, FORM 4
 
Authors :  D. J. Leibly, G. S. Waldo, T. O. Yeates
Date :  21 Aug 14  (Deposition) - 18 Feb 15  (Release) - 27 Jan 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.60
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  Fluorescent Protei, Fluorescent Protein (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 D21H/K26C
    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): AB  
Biological Unit 2 (1x):   CD

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (2, 7)
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
2CU3Ligand/IonCOPPER (II) ION
Biological Unit 1 (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
2CU-1Ligand/IonCOPPER (II) ION
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
2CU-1Ligand/IonCOPPER (II) ION

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:19 , HIS A:21 , CYS A:26 , ASP B:19 , HIS B:21binding site for residue CU A 301
2AC2SOFTWAREHIS A:25binding site for residue CU A 302
3AC3SOFTWAREHIS C:21 , HIS D:21binding site for residue CU C 301
4AC4SOFTWARELEU B:18 , LEU B:42 , LEU B:44 , LEU B:60 , VAL B:61 , THR B:62 , THR B:63 , VAL B:68 , GLN B:69 , GLN B:94 , ARG B:96 , VAL B:112 , PHE B:145 , THR B:203 , LEU B:220 , GLU B:222binding site for Di-peptide LEU B 64 and CRO B 66
5AC5SOFTWARELEU B:42 , LEU B:44 , VAL B:61 , THR B:62 , LEU B:64 , GLN B:69 , CYS B:70 , PHE B:71 , GLN B:94 , ARG B:96 , VAL B:112 , ASN B:121 , PHE B:145 , THR B:203 , LEU B:220 , GLU B:222binding site for Di-peptide CRO B 66 and VAL B 68
6AC6SOFTWARELEU C:44 , PHE C:46 , LEU C:60 , VAL C:61 , THR C:62 , THR C:63 , VAL C:68 , GLN C:69 , GLN C:94 , ARG C:96 , ASN C:121 , ILE C:123 , PHE C:145 , THR C:203 , MET C:218 , GLU C:222binding site for Di-peptide LEU C 64 and CRO C 66
7AC7SOFTWARELEU C:44 , VAL C:61 , THR C:62 , THR C:63 , LEU C:64 , GLN C:69 , CYS C:70 , PHE C:71 , GLN C:94 , ARG C:96 , ASN C:121 , PHE C:145 , THR C:203 , GLU C:222binding site for Di-peptide CRO C 66 and VAL C 68
8AC8SOFTWARELEU D:18 , LEU D:60 , VAL D:61 , THR D:62 , THR D:63 , VAL D:68 , GLN D:69 , GLN D:94 , ARG D:96 , ASN D:121 , ILE D:123 , PHE D:145 , VAL D:150 , THR D:203 , MET D:218 , GLU D:222binding site for Di-peptide LEU D 64 and CRO D 66
9AC9SOFTWAREVAL D:61 , THR D:62 , THR D:63 , LEU D:64 , GLN D:69 , CYS D:70 , GLN D:94 , ARG D:96 , LEU D:119 , ASN D:121 , PHE D:145 , VAL D:150 , THR D:203 , GLU D:222binding site for Di-peptide CRO D 66 and VAL D 68

(-) SS Bonds  (2, 2)

Asymmetric Unit
No.Residues
1A:26 -B:26
2C:26 -D:26

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4W7A)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4W7A)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4W7A)

(-) Exons   (0, 0)

(no "Exon" information available for 4W7A)

(-) 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:220
                                                                                                                                                                                                                                                            
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhh....eeeeeeeee...eeeeeeeeeee....eeeeeeee.......hhhhh....hhhhh.........hhhhhh..eeeeeeeee....eeeeeeeeeee..eeeeeeeeeee...................eeeeeeee....eeeeeeeeeee.....eeeeeeeeeeee.........eeeeeeeeee........eeeeeeeeeee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4w7a A   4 GEELFTGVVPILIELDGHVNGHCFFVRGEGEGDATIGKLSLKFIATTGKLPVPWPTLVTTxVQCFSRYPDHMKRHDFFKSAMGYVQERTIYFKDDGTYKTRAEVKFEGDTLVNRIELKGIDFKEDGNILGHKLEYNFNSHKVYITADKQNNGIKANFTIRHNVEDGSVQLADHYQQNTPIGDGDLPDDHYLSTQTILSKDLNEKRDHMVLLEYVTAAGIT 230
                                    13        23        33        43        53        63||      76        86 ||     98       108       118       128       138       148       158       168       178       188  ||   200       210       220       230
                                                                                      63||                  88|                                                                                                 191|                                    
                                                                                       66-CRO                91                                                                                                  194                                    
                                                                                        68                                                                                                                                                              


Chain B from PDB  Type:PROTEIN  Length:223
                                                                                                                                                                                                                                                               
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhh.eeeeeeeeeeee..eeeeeeeeeeee....eeeeeeee.......hhhhh...................hhhhhh...eeeeeeeee....eeeeeeeeeee..eeeeeeeeeee...................eeeeeeee....eeeeeeeeeee.....eeeeeeeeeeee...........eeeeeeeeee........eeeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4w7a B   4 GEELFTGVVPILIELDGHVNGHCFFVRGEGEGDATIGKLSLKFIATTGKLPVPWPTLVTTLxVQCFSRYPDHMKRHDFFKSAMEGYVQERTIYFKDDGTYKTRAEVKFEGDTLVNRIELKGIDFKEDGNILGHKLEYNFNSHKVYITADKQNNGIKANFTIRHNVEDGSVQLADHYQQNTPIGDGPVDLPDDHYLSTQTILSKDLNEKRDHMVLLEYVTAAGI 229
                                    13        23        33        43        53        63|||     75        85  ||    96       106       116       126       136       146       156       166       176       186       196       206       216       226   
                                                                                       64||                  88|                                                                                                                                           
                                                                                        66-CRO                90                                                                                                                                           
                                                                                         68                                                                                                                                                                


Chain C from PDB  Type:PROTEIN  Length:221
                                                                                                                                                                                                                                                             
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeeeeeeeeee..eeeeeeeeeeee....eeeeeeee........hhhhhh.............hhhhhhhhhh...eeeeeeeee....eeeeeeeeeee..eeeeeeeeeee...................eeeeeeee....eeeeeeeeeee.....eeeeeeeeeeee........eeeeeeeeee........eeeeeeeeeee... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4w7a C   4 GEELFTGVVPILIELDGHVNGHCFFVRGEGEGDATIGKLSLKFIATTGKLPVPWPTLVTTLxVQCFSRYPDHMKRHDFFKSAMEGYVQERTIYFKDDGTYKTRAEVKFEGDTLVNRIELKGIDFKEDGNILGHKLEYNFNSHKVYITADKQNNGIKANFTIRHNVEDGSVQLADHYQQNTPIGDDLPDDHYLSTQTILSKDLNEKRDHMVLLEYVTAAGIT 230
                                    13        23        33        43        53        63|||     75        85  ||    96       106       116       126       136       146       156       166       176       186   ||  199       209       219       229 
                                                                                       64||                  88|                                                                                                 190|                                    
                                                                                        66-CRO                90                                                                                                  194                                    
                                                                                         68                                                                                                                                                              


Chain D from PDB  Type:PROTEIN  Length:217
                                                                                                                                                                                                                                                         
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhh.eeeeeeeeeeee..eeeeeeeeeeee....eeeeeeee.......hhhhh...............hhhhh.....eeeeeeeee....eeeeeeeeeee..eeeeeeeeeee...................eeeeeeee....eeeeeeeeeee.....eeeeeeeeeeee.......eeeeeeeeee........eeeeeeeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4w7a D   4 GEELFTGVVPILIELDGHVNGHCFFVRGEGEGDATIGKLSLKFIATTGKLPVPWPTLVTTLxVQCFSRYPDHMKRHDFFKSGYVQERTIYFKDDGTYKTRAEVKFEGDTLVNRIELKGIDFKEDGNILGHKLEYNFNSHKVYITADKQNNGIKANFTIRHNVEDGSVQLADHYQQNTPIGDLPDDHYLSTQTILSKDLNEKRDHMVLLEYVTAAGIT 230
                                    13        23        33        43        53        63|||     75        85||      99       109       119       129       139       149       159       169       179       189|      203       213       223       
                                                                                       64||                86|                                                                                               189|                                    
                                                                                        66-CRO              91                                                                                                194                                    
                                                                                         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 4W7A)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4W7A)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4W7A)

(-) Gene Ontology  (0, 0)

Asymmetric Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 4W7A)

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(-) Related Entries Specified in the PDB File

4w69 4w6a 4w6b 4w6c 4w6d 4w6f 4w6g 4w6h 4w6i 4w6j 4w6k 4w6l 4w6m 4w6n 4w6o 4w6p 4w6r 4w6s 4w6t 4w6u 4w72 4w73 4w74 4w75 4w76 4w77 4w7c 4w7d 4w7e 4w7f 4w7r 4w7x