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(-) Description

Title :  CRYSTAL STRUCTURE OF AN ANCESTRAL GFP-LIKE PROTEIN
 
Authors :  H. Kim, R. Fromme, R. M. Wachter
Date :  27 Feb 12  (Deposition) - 27 Feb 13  (Release) - 22 Apr 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.40
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Beta Barrel, Luminescent Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. Kim, T. Zou, C. Modi, K. Dorner, T. J. Grunkemeyer, L. Chen, R. Fromme M. V. Matz, S. B. Ozkan, R. M. Wachter
A Hinge Migration Mechanism Unlocks The Evolution Of Green-To-Red Photoconversion In Gfp-Like Proteins.
Structure V. 23 34 2015
PubMed-ID: 25565105  |  Reference-DOI: 10.1016/J.STR.2014.11.011

(-) Compounds

Molecule 1 - GREEN FLUORESCENT PROTEIN
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PGEM-T
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Organism Common: ARTIFICIAL
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (2, 7)
No.NameCountTypeFull Name
1CR84Mod. Amino Acid2-[1-AMINO-2-(1H-IMIDAZOL-5-YL)ETHYL]-1-(CARBOXYMETHYL)-4-[(4-OXOCYCLOHEXA-2,5-DIEN-1-YLIDENE)METHYL]-1H-IMIDAZOL-5-OLATE
2SO43Ligand/IonSULFATE ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREVAL A:148 , ARG A:149 , ASP A:150 , HOH A:425 , HOH A:438 , HOH A:637 , HOH A:646 , GLY B:167BINDING SITE FOR RESIDUE SO4 A 301
2AC2SOFTWAREGLY A:167 , ARG B:149 , ASP B:150 , HOH B:424 , HOH B:519 , HOH B:560BINDING SITE FOR RESIDUE SO4 B 301
3AC3SOFTWAREGLY C:167 , ASP D:150 , HOH D:407 , HOH D:452 , HOH D:600 , HOH D:651 , HOH D:661BINDING SITE FOR RESIDUE SO4 D 301

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (8, 8)

Asymmetric/Biological Unit
No.Residues
1Ala A:48 -Pro A:49
2Phe A:83 -Pro A:84
3Ala B:48 -Pro B:49
4Phe B:83 -Pro B:84
5Ala C:48 -Pro C:49
6Phe C:83 -Pro C:84
7Ala D:48 -Pro D:49
8Phe D:83 -Pro D:84

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4DXM)

(-) Sequences/Alignments

Asymmetric/Biological 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 ......eeeeeeeeeee..eeeeeeeeeeee....eeeeeeeeee.......hhhhhh...............hhhhhh....eeeeeeeee....eeeeeeeeeee..eeeeeeeeeee............eeee..eeeeeeee..eeeeeeeeeeee....eeeeeeeeeeee.........eeeeeeeeeeee.....eeeeeeeeeee....... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4dxm A   2 SVIKSDMKIKLRMEGTVNGHKFVIEGEGEGKPYEGTQTMNLKVKEGAPLPFAYDILTTAFhNRVFTKYPKDIPDYFKQSFPEGYSWERSMTFEDGGICTATSDITLEGDCFFYEIRFDGVNFPPNGPVMQKKTLKWEPSTEKMYVRDGVLMGDVNMALLLEGGGHYRCDFKTTYKAKKGVQLPDYHFVDHRIEILSHDKDYNNVKLYEHAVARYSMLPRQ 223
                                    11        21        31        41        51        61||      73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223
                                                                                      61||                                                                                                                                                              
                                                                                       63-CR8                                                                                                                                                           
                                                                                        65                                                                                                                                                              


Chain B from PDB  Type:PROTEIN  Length:221
                                                                                                                                                                                                                                                             
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeeeeeeeee..eeeeeeeeeeee....eeeeeeeeee.......hhhhhh...............hhhhhh....eeeeeeeee....eeeeeeeeeee..eeeeeeeeeee............eeee..eeeeeeee..eeeeeeeeeeee....eeeeeeeeeeee.........eeeeeeeeeeee.hhh.eeeeeeeeeee......... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4dxm B   3 VIKSDMKIKLRMEGTVNGHKFVIEGEGEGKPYEGTQTMNLKVKEGAPLPFAYDILTTAFhNRVFTKYPKDIPDYFKQSFPEGYSWERSMTFEDGGICTATSDITLEGDCFFYEIRFDGVNFPPNGPVMQKKTLKWEPSTEKMYVRDGVLMGDVNMALLLEGGGHYRCDFKTTYKAKKGVQLPDYHFVDHRIEILSHDKDYNNVKLYEHAVARYSMLPRQAK 225
                                    12        22        32        42        52        63|       74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224 
                                                                                     61||                                                                                                                                                                
                                                                                      63-CR8                                                                                                                                                             
                                                                                       65                                                                                                                                                                


Chain C from PDB  Type:PROTEIN  Length:220
                                                                                                                                                                                                                                                            
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeeeeeeeee..eeeeeeeeeeee....eeeeeeeeee.......hhhhhh...............hhhhhh....eeeeeeeee....eeeeeeeeeee..eeeeeeeeeee............eeee..eeeeeeee..eeeeeeeeeeee....eeeeeeeeeeee.........eeeeeeeeeeee.....eeeeeeeeeee....... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4dxm C   2 SVIKSDMKIKLRMEGTVNGHKFVIEGEGEGKPYEGTQTMNLKVKEGAPLPFAYDILTTAFhNRVFTKYPKDIPDYFKQSFPEGYSWERSMTFEDGGICTATSDITLEGDCFFYEIRFDGVNFPPNGPVMQKKTLKWEPSTEKMYVRDGVLMGDVNMALLLEGGGHYRCDFKTTYKAKKGVQLPDYHFVDHRIEILSHDKDYNNVKLYEHAVARYSMLPRQ 223
                                    11        21        31        41        51        61||      73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223
                                                                                      61||                                                                                                                                                              
                                                                                       63-CR8                                                                                                                                                           
                                                                                        65                                                                                                                                                              


Chain D from PDB  Type:PROTEIN  Length:221
                                                                                                                                                                                                                                                             
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeeeeeeeee..eeeeeeeeeeee....eeeeeeeeee.......hhhhhh...............hhhhhh....eeeeeeeee....eeeeeeeeeee..eeeeeeeeeee............eeee..eeeeeeee..eeeeeeeeeeee....eeeeeeeeeeee.........eeeeeeeeeeee.....eeeeeeeeeee........ Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4dxm D   2 SVIKSDMKIKLRMEGTVNGHKFVIEGEGEGKPYEGTQTMNLKVKEGAPLPFAYDILTTAFhNRVFTKYPKDIPDYFKQSFPEGYSWERSMTFEDGGICTATSDITLEGDCFFYEIRFDGVNFPPNGPVMQKKTLKWEPSTEKMYVRDGVLMGDVNMALLLEGGGHYRCDFKTTYKAKKGVQLPDYHFVDHRIEILSHDKDYNNVKLYEHAVARYSMLPRQA 224
                                    11        21        31        41        51        61||      73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223 
                                                                                      61||                                                                                                                                                               
                                                                                       63-CR8                                                                                                                                                            
                                                                                        65
   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  (0, 0)

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

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (0, 0)

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

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  Cis Peptide Bonds
    Ala A:48 - Pro A:49   [ RasMol ]  
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    Ala C:48 - Pro C:49   [ RasMol ]  
    Ala D:48 - Pro D:49   [ RasMol ]  
    Phe A:83 - Pro A:84   [ RasMol ]  
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(-) Related Entries Specified in the PDB File

4dxi 4dxn 4dxo 4dxp 4dxq