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(-) Description

Title :  CRYSTAL STRUCTURE OF FULL-LENGTH SPLIT GFP MUTANT E124H/K126H COPPER MEDIATED DIMER, P 21 SPACE GROUP
 
Authors :  D. J. Leibly, G. S. Waldo, T. O. Yeates
Date :  22 Aug 14  (Deposition) - 04 Mar 15  (Release) - 27 Jan 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  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 E124H/K126C
    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  (3, 20)

Asymmetric Unit (3, 20)
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
2CU2Ligand/IonCOPPER (II) ION
3EDO14Ligand/Ion1,2-ETHANEDIOL
Biological Unit 1 (2, 9)
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
3EDO7Ligand/Ion1,2-ETHANEDIOL
Biological Unit 2 (2, 9)
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
3EDO7Ligand/Ion1,2-ETHANEDIOL

(-) Sites  (16, 16)

Asymmetric Unit (16, 16)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHIS A:124 , HIS A:126 , HIS B:124 , HIS B:126binding site for residue CU A 301
02AC2SOFTWAREPHE A:145 , SER A:147 , GLN A:204 , THR A:205 , PHE B:145 , ASN B:146 , GLN B:204 , THR B:205 , HOH B:402binding site for residue EDO A 302
03AC3SOFTWAREALA A:87 , GLU A:90 , GLY A:91 , PRO A:187 , ILE A:188 , GLY A:189 , ASP A:190 , GLY A:191binding site for residue EDO A 303
04AC4SOFTWAREASN A:159 , PRO A:192 , VAL A:193 , LEU A:195binding site for residue EDO A 304
05AC5SOFTWAREILE A:39 , ARG A:73 , SER B:208 , LYS B:209 , LEU B:211binding site for residue EDO B 301
06AC6SOFTWAREHIS A:126 , ASP B:21 , GLY B:24 , HIS B:126 , GLY B:127binding site for residue EDO B 302
07AC7SOFTWAREHIS B:77 , ALA B:227 , GLY B:228 , EDO B:304binding site for residue EDO B 303
08AC8SOFTWAREHIS B:77 , GLY B:228 , EDO B:303 , HOH B:452binding site for residue EDO B 304
09AC9SOFTWAREHIS C:124 , HIS C:126 , HIS D:124 , HIS D:126binding site for residue CU C 301
10AD1SOFTWAREPRO C:56 , TRP C:57 , ASP C:216 , HOH C:443 , HOH C:471binding site for residue EDO C 302
11AD2SOFTWARELEU C:7 , ASP C:117 , HOH C:482binding site for residue EDO C 303
12AD3SOFTWARESER C:208 , LYS C:209 , ILE D:39 , ARG D:73binding site for residue EDO D 301
13AD4SOFTWAREALA D:87 , GLU D:90 , GLY D:91 , PRO D:187 , ILE D:188 , GLY D:189 , ASP D:190 , GLY D:191binding site for residue EDO D 302
14AD5SOFTWAREGLY D:4 , GLU D:5 , SER D:86binding site for residue EDO D 303
15AD6SOFTWARETRP D:57 , ASP D:216 , HOH D:421binding site for residue EDO D 304
16AD7SOFTWARETYR D:99 , LYS D:101 , ASP D:180 , TYR D:182binding site for residue EDO D 305

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4W7R)

(-) Cis Peptide Bonds  (5, 5)

Asymmetric Unit
No.Residues
1Met A:88 -Pro A:89
2Met B:88 -Pro B:89
3Asp B:190 -Gly B:191
4Met C:88 -Pro C:89
5Met D:88 -Pro D:89

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4W7R)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4W7R)

(-) Exons   (0, 0)

(no "Exon" information available for 4W7R)

(-) 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:226
                                                                                                                                                                                                                                                                  
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhh..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
                 4w7r A   1 MRKGEELFTGVVPILIELDGDVNGHKFFVRGEGEGDATIGKLSLKFIATTGKLPVPWPTLVTTLxVQAFSRYPDHMKRHDFFKSAMPEGYVQERTIYFKDDGTYKTRAEVKFEGDTLVNRIHLHGIDFKEDGNILGHKLEYNFNSHKVYITADKQNNGIKANFTIRHNVEDGSVQLADHYQQNTPIGDGPVDLPDDHYLSTQTILSKDLNEKRDHMVLLEYVTAAG 228
                                    10        20        30        40        50        60   |||  72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222      
                                                                                          64||                                                                                                                                                                
                                                                                           66-CRO                                                                                                                                                             
                                                                                            68                                                                                                                                                                


Chain B from PDB  Type:PROTEIN  Length:225
                                                                                                                                                                                                                                                                 
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhh..eeeeeeeeeee..eeeeeeeeeeee....eeeeeeee.......hhhhhh....hhhhh..hhhhhhhhhhhhh....eeeeeeeee....eeeeeeeeeee..eeeeeeeeeee...................eeeeeeeehhhheeeeeeeeeee.....eeeeeeeeeeee...........eeeeeeeeee........eeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4w7r B   2 RKGEELFTGVVPILIELDGDVNGHKFFVRGEGEGDATIGKLSLKFIATTGKLPVPWPTLVTTLxVQAFSRYPDHMKRHDFFKSAMPEGYVQERTIYFKDDGTYKTRAEVKFEGDTLVNRIHLHGIDFKEDGNILGHKLEYNFNSHKVYITADKQNNGIKANFTIRHNVEDGSVQLADHYQQNTPIGDGPVDLPDDHYLSTQTILSKDLNEKRDHMVLLEYVTAAG 228
                                    11        21        31        41        51        61  |||   73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223     
                                                                                         64||                                                                                                                                                                
                                                                                          66-CRO                                                                                                                                                             
                                                                                           68                                                                                                                                                                


Chain C from PDB  Type:PROTEIN  Length:226
                                                                                                                                                                                                                                                                  
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhh..eeeeeeeeeee..eeeeeeeeeeee....eeeeeeee.......hhhhhh....hhhhh..hhhhhhhhhhhhh....eeeeeeeee....eeeeeeeeeee..eeeeeeeeeee...................eeeeeeeehhhheeeeeeeeeee.....eeeeeeeeeeee...........eeeeeeeeee........eeeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4w7r C   2 RKGEELFTGVVPILIELDGDVNGHKFFVRGEGEGDATIGKLSLKFIATTGKLPVPWPTLVTTLxVQAFSRYPDHMKRHDFFKSAMPEGYVQERTIYFKDDGTYKTRAEVKFEGDTLVNRIHLHGIDFKEDGNILGHKLEYNFNSHKVYITADKQNNGIKANFTIRHNVEDGSVQLADHYQQNTPIGDGPVDLPDDHYLSTQTILSKDLNEKRDHMVLLEYVTAAGI 229
                                    11        21        31        41        51        61  |||   73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223      
                                                                                         64||                                                                                                                                                                 
                                                                                          66-CRO                                                                                                                                                              
                                                                                           68                                                                                                                                                                 


Chain D from PDB  Type:PROTEIN  Length:226
                                                                                                                                                                                                                                                                  
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhh..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
                 4w7r D   2 RKGEELFTGVVPILIELDGDVNGHKFFVRGEGEGDATIGKLSLKFIATTGKLPVPWPTLVTTLxVQAFSRYPDHMKRHDFFKSAMPEGYVQERTIYFKDDGTYKTRAEVKFEGDTLVNRIHLHGIDFKEDGNILGHKLEYNFNSHKVYITADKQNNGIKANFTIRHNVEDGSVQLADHYQQNTPIGDGPVDLPDDHYLSTQTILSKDLNEKRDHMVLLEYVTAAGI 229
                                    11        21        31        41        51        61  |||   73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223      
                                                                                         64||                                                                                                                                                                 
                                                                                          66-CRO                                                                                                                                                              
                                                                                           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 4W7R)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4W7R)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4W7R)

(-) Gene Ontology  (0, 0)

Asymmetric Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 4W7R)

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  Cis Peptide Bonds
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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 4w6n 4w6o 4w6p 4w6r 4w6s 4w6t 4w6u 4w72 4w73 4w74 4w75 4w76 4w77 4w7a 4w7c 4w7d 4w7e 4w7f 4w7x