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(-) Description

Title :  RATIONAL DESIGN OF ENHANCED PHOTORESISTANCE IN A PHOTOSWITCHABLE FLUORESCENT PROTEIN
 
Authors :  C. Duan, V. Adam, M. Byrdin, D. Bourgeois
Date :  23 Aug 14  (Deposition) - 04 Feb 15  (Release) - 11 Nov 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Beta-Barrel, Fluorescent Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. Duan, M. Byrdin, M. El Khatib, X. Henry, V. Adam, D. Bourgeois
Rational Design Of Enhanced Photoresistance In A Photoswitchable Fluorescent Protein.
Methods Appl Fluoresc V. 3 2015
PubMed: search  |  Reference-DOI: 10.1088/2050-6120/3/1/014004

(-) Compounds

Molecule 1 - GREEN TO RED PHOTOCONVERTIBLE GFP-LIKE PROTEIN EOSFP
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PQE32
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Mutation: YES
    Organism Common: LOBED BRAIN CORAL
    Organism Scientific: LOBOPHYLLIA HEMPRICHII
    Organism Taxid: 46758

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 23)

Asymmetric/Biological Unit (3, 23)
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
2SO34Ligand/IonSULFITE ION
3SO415Ligand/IonSULFATE ION

(-) Sites  (19, 19)

Asymmetric Unit (19, 19)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASN A:17 , HIS A:22 , HOH A:518 , ARG C:119BINDING SITE FOR RESIDUE SO4 A 301
02AC2SOFTWAREASP A:202 , LYS A:203 , HOH A:621 , HOH A:635BINDING SITE FOR RESIDUE SO4 A 302
03AC3SOFTWARELYS A:182 , GLY A:183BINDING SITE FOR RESIDUE SO4 A 303
04AC4SOFTWAREGLU A:197 , LEU A:199 , HOH A:614 , HOH A:623 , HOH A:633BINDING SITE FOR RESIDUE SO3 A 304
05AC5SOFTWAREARG A:149 , ASP A:150 , HOH A:416 , HOH A:462 , ALA B:167BINDING SITE FOR RESIDUE SO4 A 305
06AC6SOFTWAREPRO A:221 , HOH A:538 , HOH A:601 , GLU B:197BINDING SITE FOR RESIDUE SO3 A 306
07AC7SOFTWAREALA A:167 , HOH A:618 , ARG B:149 , ASP B:150 , HOH B:428 , HOH B:513 , HOH B:516BINDING SITE FOR RESIDUE SO4 B 301
08AC8SOFTWAREASP B:202 , LYS B:203BINDING SITE FOR RESIDUE SO4 B 302
09AC9SOFTWARELYS B:182 , GLY B:183 , HOH B:496 , HOH B:525 , HOH B:530BINDING SITE FOR RESIDUE SO4 B 303
10BC1SOFTWAREHOH A:492 , HOH A:545 , ASN C:17 , HIS C:22 , HIS C:121BINDING SITE FOR RESIDUE SO4 C 301
11BC2SOFTWAREASP C:202 , LYS C:203 , HOH C:568BINDING SITE FOR RESIDUE SO4 C 302
12BC3SOFTWAREPHE A:34 , GLU A:70 , HOH A:437 , HOH A:475 , TYR C:78 , GLY C:151 , HOH C:454 , HOH C:505BINDING SITE FOR RESIDUE SO4 C 303
13BC4SOFTWARECYS C:195 , GLU C:197 , HOH C:537 , PRO D:221BINDING SITE FOR RESIDUE SO3 C 304
14BC5SOFTWAREASN B:17 , HIS B:22 , ARG D:119 , HOH D:428 , HOH D:463 , HOH D:554BINDING SITE FOR RESIDUE SO4 D 301
15BC6SOFTWAREALA C:167 , ARG D:149 , ASP D:150 , HOH D:430 , HOH D:513BINDING SITE FOR RESIDUE SO4 D 302
16BC7SOFTWAREHIS D:22 , HIS D:121 , HOH D:540 , HOH D:570BINDING SITE FOR RESIDUE SO4 D 303
17BC8SOFTWAREASP D:202 , LYS D:203BINDING SITE FOR RESIDUE SO4 D 304
18BC9SOFTWARELYS D:182 , GLY D:183BINDING SITE FOR RESIDUE SO4 D 305
19CC1SOFTWAREPRO C:221 , GLU D:197BINDING SITE FOR RESIDUE SO3 D 306

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4R6B)

(-) Cis Peptide Bonds  (12, 12)

Asymmetric/Biological Unit
No.Residues
1Gly A:48 -Pro A:49
2Phe A:83 -Pro A:84
3Leu A:220 -Pro A:221
4Gly B:48 -Pro B:49
5Phe B:83 -Pro B:84
6Leu B:220 -Pro B:221
7Gly C:48 -Pro C:49
8Phe C:83 -Pro C:84
9Leu C:220 -Pro C:221
10Gly D:48 -Pro D:49
11Phe D:83 -Pro D:84
12Leu D:220 -Pro D:221

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4R6B)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4R6B)

(-) Exons   (0, 0)

(no "Exon" information available for 4R6B)

(-) 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:221
                                                                                                                                                                                                                                                             
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeeeeeeeee..eeeeeeeeeeeehhh.eeeeeeeeee......hhhhhhhhh...............hhhhh...eeeeeeeee....eeeeeeeeeee..eeeeeeeeeee............eeee..eeeeeeee..eeeeeeeeeeee....eeeeeeeeeeee..........eeeeeeeeeeee.....eeeeeeeeeee...... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4r6b A   1 MSAIKPDMKINLRMEGNVNGHHFVIDGDGTGKPFEGKQSMDLEVKEGGPLPFAFDILTTAFhNRVFAEYPDHIQDYFKQSFPKGYSWERSLTFEDGGICIARNDITMEGDTFYNKVRFHGVNFPANGPVMQKKTLKWEPSTEKMYVRDGVLTGDITAALLLEGNAHYRCDSRTTYKAKEKGVKLPGYHLVDHCIEILSHDKDYNKVKLYEHAVAHSGLPDN 223
                                    10        20        30        40        50        60||      72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222 
                                                                                       61|                                                                                                                                                               
                                                                                        64-CR8                                                                                                                                                           


Chain B from PDB  Type:PROTEIN  Length:220
                                                                                                                                                                                                                                                            
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeeeeeeeee..eeeeeeeeeeeehhh.eeeeeeeeee......hhhhhh..................hhhhh...eeeeeeeee....eeeeeeeeeee..eeeeeeeeeee............eeee..eeeeeeee..eeeeeeeeeeee....eeeeeeeeeeee..........eeeeeeeeeeee.....eeeeeeeeeee...... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4r6b B   2 SAIKPDMKINLRMEGNVNGHHFVIDGDGTGKPFEGKQSMDLEVKEGGPLPFAFDILTTAFhNRVFAEYPDHIQDYFKQSFPKGYSWERSLTFEDGGICIARNDITMEGDTFYNKVRFHGVNFPANGPVMQKKTLKWEPSTEKMYVRDGVLTGDITAALLLEGNAHYRCDSRTTYKAKEKGVKLPGYHLVDHCIEILSHDKDYNKVKLYEHAVAHSGLPDN 223
                                    11        21        31        41        51        61|       73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223
                                                                                      61|                                                                                                                                                               
                                                                                       64-CR8                                                                                                                                                           


Chain C from PDB  Type:PROTEIN  Length:223
                                                                                                                                                                                                                                                               
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........eeeeeeeeeee..eeeeeeeeeeeehhh.eeeeeeeeee......hhhhhh..........................eeeeeeeee....eeeeeeeeeee..eeeeeeeeeee............eeee..eeeeeeee..eeeeeeeeeeee....eeeeeeeeeeee..........eeeeeeeeeeee.....eeeeeeeeeee...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4r6b C  -1 HHMSAIKPDMKINLRMEGNVNGHHFVIDGDGTGKPFEGKQSMDLEVKEGGPLPFAFDILTTAFhNRVFAEYPDHIQDYFKQSFPKGYSWERSLTFEDGGICIARNDITMEGDTFYNKVRFHGVNFPANGPVMQKKTLKWEPSTEKMYVRDGVLTGDITAALLLEGNAHYRCDSRTTYKAKEKGVKLPGYHLVDHCIEILSHDKDYNKVKLYEHAVAHSGLPDN 223
                                     8        18        28        38        48        58  ||    70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220   
                                                                                         61|                                                                                                                                                               
                                                                                          64-CR8                                                                                                                                                           


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..........................eeeeeeeee....eeeeeeeeeee..eeeeeeeeeee............eeee..eeeeeeee..eeeeeeeeeeee....eeeeeeeeeeee..........eeeeeeeeeeee.....eeeeeeeeeee...... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4r6b D   1 MSAIKPDMKINLRMEGNVNGHHFVIDGDGTGKPFEGKQSMDLEVKEGGPLPFAFDILTTAFhNRVFAEYPDHIQDYFKQSFPKGYSWERSLTFEDGGICIARNDITMEGDTFYNKVRFHGVNFPANGPVMQKKTLKWEPSTEKMYVRDGVLTGDITAALLLEGNAHYRCDSRTTYKAKEKGVKLPGYHLVDHCIEILSHDKDYNKVKLYEHAVAHSGLPDN 223
                                    10        20        30        40        50        60||      72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222 
                                                                                       61|                                                                                                                                                               
                                                                                        64-CR8
   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 4R6B)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4R6B)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4R6B)

(-) Gene Ontology  (2, 2)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
    Gly A:48 - Pro A:49   [ RasMol ]  
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    Gly C:48 - Pro C:49   [ RasMol ]  
    Gly D:48 - Pro D:49   [ RasMol ]  
    Leu A:220 - Pro A:221   [ RasMol ]  
    Leu B:220 - Pro B:221   [ RasMol ]  
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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/TrEMBL
        Q5S6Z9_LOBHE | Q5S6Z9: 1zux 2btj 2vvh 2vvi 2vvj 3p8u 3s05 3tmr 3tmt 4ljb 4ljc 4ljd 4oy4 5dtl 5fvf 5fvg 5fvi

(-) Related Entries Specified in the PDB File

1zux WILD-TYPE PROTEIN EOSFP IN ITS NATIVE GREEN FORM
2btj WILD-TYPE PROTEIN EOSFP IN ITS PHOTOCONVERTED RED FORM
2vvh PARENT PROTEIN IRISFP IN ITS NATIVE GREEN FORM
2vvi PARENT PROTEIN IRISFP IN ITS PHOTOSWITCHED FORM, TRANS CONFORMATION
2vvj PARENT PROTEIN IRISFP PHOTOCONVERTED TO ITS RED FORM
3p8u WILD-TYPE PROTEIN EOSFP IN ITS MONOMERIC FORM, MEOSFP
3tmr PARENT PROTEIN IRISFP UNDER VERY LOW X-RAY DOSE, SHOWING A PLANAR CHROMOPHORE
3tmt PARENT PROTEIN IRISFP WITH AN X-RAY INDUCED DISTORTED CHROMOPHORE
4ljb PARENT PROTEIN IRISFP PHOTOBLEACHED UNDER HIGH LASER- INTENSITY
4ljc PARENT PROTEIN IRISFP PHOTOBLEACHED X-RAYS
4ljd PARENT PROTEIN IRISFP PHOTOBLEACHED UNDER LOW INTENSITY LASER-LIGHT