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(-) Description

Title :  IRISFP, DISTORTED CHROMOPHORE
 
Authors :  V. Adam, P. Carpentier, A. Roy, M. Field, D. Bourgeois
Date :  31 Aug 11  (Deposition) - 16 Nov 11  (Release) - 30 Nov 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Beta-Can, Fluorescent Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Roy, M. J. Field, V. Adam, D. Bourgeois
The Nature Of Transient Dark States In A Photoactivatable Fluorescent Protein.
J. Am. Chem. Soc. V. 133 18586 2011
PubMed-ID: 22039963  |  Reference-DOI: 10.1021/JA2085355

(-) Compounds

Molecule 1 - GREEN TO RED PHOTOCONVERTIBLE GPF-LIKE PROTEIN EOSFP
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    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  (2, 21)

Asymmetric/Biological Unit (2, 21)
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
2SO417Ligand/IonSULFATE ION

(-) Sites  (17, 17)

Asymmetric Unit (17, 17)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASN A:17 , HIS A:22 , HOH A:490 , HOH A:706 , HOH A:780BINDING SITE FOR RESIDUE SO4 A 1224
02AC2SOFTWAREASP A:202 , LYS A:203 , HOH A:806 , HOH A:1856BINDING SITE FOR RESIDUE SO4 A 1225
03AC3SOFTWAREARG A:119 , HOH A:300 , HOH A:1682 , HOH A:2243 , HOH A:2622 , HOH A:2709BINDING SITE FOR RESIDUE SO4 A 227
04AC4SOFTWAREASN A:11 , LEU A:12 , ARG A:13 , ASP A:26 , HOH A:1335 , HOH A:3183BINDING SITE FOR RESIDUE SO4 A 228
05AC5SOFTWAREASP B:202 , LYS B:203 , HOH B:595 , HOH B:3325 , HOH B:3330BINDING SITE FOR RESIDUE SO4 B 1225
06AC6SOFTWAREMET B:1 , PRO B:130 , LEU B:163 , HIS B:168 , HOH B:621 , HOH B:671 , HOH B:2277BINDING SITE FOR RESIDUE SO4 B 1224
07AC7SOFTWAREASP B:150 , GLY B:151 , HOH B:241 , HOH B:274 , HOH B:610 , HOH B:2065 , HOH B:2729BINDING SITE FOR RESIDUE SO4 B 227
08AC8SOFTWAREVAL C:148 , ARG C:149 , ASP C:150 , HOH C:283 , HOH C:369 , HOH C:1437 , HOH C:1773 , HOH C:1898BINDING SITE FOR RESIDUE SO4 C 1224
09AC9SOFTWAREASN C:17 , HIS C:22 , HIS C:121 , HOH C:504 , HOH C:1932 , ARG D:104 , ARG D:119BINDING SITE FOR RESIDUE SO4 C 1225
10BC1SOFTWAREASP C:202 , LYS C:203 , HOH C:948 , HOH C:1368 , HOH C:1458 , HOH C:1848 , HOH C:1905 , HOH C:1914 , HOH C:2751BINDING SITE FOR RESIDUE SO4 C 1226
11BC2SOFTWARELYS C:182 , GLY C:183 , HOH C:787BINDING SITE FOR RESIDUE SO4 C 1227
12BC3SOFTWAREGLU C:46 , GLY C:47 , HOH C:659 , HOH C:781 , HOH C:1945BINDING SITE FOR RESIDUE SO4 C 227
13BC4SOFTWAREARG C:119 , ASN D:17 , HIS D:22 , HIS D:121 , HOH D:646 , HOH D:731 , HOH D:1360BINDING SITE FOR RESIDUE SO4 D 1225
14BC5SOFTWAREASP D:202 , LYS D:203 , HOH D:744 , HOH D:849 , HOH D:2165 , HOH D:3132BINDING SITE FOR RESIDUE SO4 D 1226
15BC6SOFTWAREGLU D:181 , LYS D:182 , GLY D:183 , HOH D:2667BINDING SITE FOR RESIDUE SO4 D 1227
16BC7SOFTWAREGLU D:46 , GLY D:47 , HOH D:318 , HOH D:499 , HOH D:848BINDING SITE FOR RESIDUE SO4 D 227
17BC8SOFTWAREALA B:167 , HOH B:2277 , VAL D:148 , ASP D:150 , HOH D:248 , HOH D:1857BINDING SITE FOR RESIDUE SO4 D 228

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3TMT)

(-) Cis Peptide Bonds  (11, 11)

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
11Leu D:220 -Pro D:221

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3TMT)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3TMT)

(-) Exons   (0, 0)

(no "Exon" information available for 3TMT)

(-) 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:222
 aligned with Q5S6Z9_LOBHE | Q5S6Z9 from UniProtKB/TrEMBL  Length:226

    Alignment length:224
                             1                                                                                                                                                                                                                              
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219    
         Q5S6Z9_LOBHE     - -MSAIKPDMKINLRMEGNVNGHHFVIDGDGTGKPFEGKQSMDLEVKEGGPLPFAFDILTTAFHYGNRVFAEYPDHIQDYFKQSFPKGYSWERSLTFEDGGICIARNDITMEGDTFYNKVRFHGVNFPANGPVMQKKTLKWEPSTEKMYVRDGVLTGDITMALLLEGNAHYRCDFRTTYKAKEKGVKLPGYHFVDHCIEILSHDKDYNKVKLYEHAVAHSGLPDN 223
               SCOP domains d3tmta_ A: automated matches                                                                                                                                                                                                     SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eeeeeeeeeee..eeeeeeeeeee.hhh.eeeeeeeeee......hhhhhhhhh--...............hhhhh...eeeeeeeee....eeeeeeeeee...eeeeeeeeeee............eeee..eeeeeeee..eeeeeeeeeeee...eeeeeeeeeeeee..........eeeeeeeeeeee.....eeeeeeeeeee...... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3tmt A   0 HMSAIKPDMKINLRMEGNVNGHHFVIDGDGTGKPFEGKQSMDLEVKEGGPLPFAFDILTTAF--hNRVFAEYPDHIQDYFKQSFPKGYSWERSLTFEDGGICIARNDITMEGDTFYNKVRFHGVNFPANGPVMQKKTLKWEPSTEKMYVRDGVLTGDITMALLLEGNAHYRCDSRTTYKAKEKGVKLPGYHLVDHCIEILSHDKDYNKVKLYEHAVAHSGLPDN 223
                                     9        19        29        39        49        59 |  |   69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219    
                                                                                        61  |                                                                                                                                                               
                                                                                           64-CR8                                                                                                                                                           


Chain B from PDB  Type:PROTEIN  Length:221
 aligned with Q5S6Z9_LOBHE | Q5S6Z9 from UniProtKB/TrEMBL  Length:226

    Alignment length:223
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220   
         Q5S6Z9_LOBHE     1 MSAIKPDMKINLRMEGNVNGHHFVIDGDGTGKPFEGKQSMDLEVKEGGPLPFAFDILTTAFHYGNRVFAEYPDHIQDYFKQSFPKGYSWERSLTFEDGGICIARNDITMEGDTFYNKVRFHGVNFPANGPVMQKKTLKWEPSTEKMYVRDGVLTGDITMALLLEGNAHYRCDFRTTYKAKEKGVKLPGYHFVDHCIEILSHDKDYNKVKLYEHAVAHSGLPDN 223
               SCOP domains d3tmtb_ B: automated matches                                                                                                                                                                                                    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
                 3tmt B   1 MSAIKPDMKINLRMEGNVNGHHFVIDGDGTGKPFEGKQSMDLEVKEGGPLPFAFDILTTAF--hNRVFAEYPDHIQDYFKQSFPKGYSWERSLTFEDGGICIARNDITMEGDTFYNKVRFHGVNFPANGPVMQKKTLKWEPSTEKMYVRDGVLTGDITMALLLEGNAHYRCDSRTTYKAKEKGVKLPGYHLVDHCIEILSHDKDYNKVKLYEHAVAHSGLPDN 223
                                    10        20        30        40        50        60|  |    70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220   
                                                                                       61  |                                                                                                                                                               
                                                                                          64-CR8                                                                                                                                                           


Chain C from PDB  Type:PROTEIN  Length:220
 aligned with Q5S6Z9_LOBHE | Q5S6Z9 from UniProtKB/TrEMBL  Length:226

    Alignment length:222
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221  
         Q5S6Z9_LOBHE     2 SAIKPDMKINLRMEGNVNGHHFVIDGDGTGKPFEGKQSMDLEVKEGGPLPFAFDILTTAFHYGNRVFAEYPDHIQDYFKQSFPKGYSWERSLTFEDGGICIARNDITMEGDTFYNKVRFHGVNFPANGPVMQKKTLKWEPSTEKMYVRDGVLTGDITMALLLEGNAHYRCDFRTTYKAKEKGVKLPGYHFVDHCIEILSHDKDYNKVKLYEHAVAHSGLPDN 223
               SCOP domains d3tmtc_ C: automated matches                                                                                                                                                                                                   SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ......eeeeeeeeeee..eeeeeeeeeee.hhh.eeeeeeeeee......hhhhhhhhh--.....ee......hhhhhh....eeeeeeeee....eeeeeeeeeee..eeeeeeeeeee............eeee..eeeeeeee..eeeeeeeeeeee....eeeeeeeeeeee..........eeeeeeeeeeee.....eeeeeeeeeee...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3tmt C   2 SAIKPDMKINLRMEGNVNGHHFVIDGDGTGKPFEGKQSMDLEVKEGGPLPFAFDILTTAF--hNRVFAEYPDHIQDYFKQSFPKGYSWERSLTFEDGGICIARNDITMEGDTFYNKVRFHGVNFPANGPVMQKKTLKWEPSTEKMYVRDGVLTGDITMALLLEGNAHYRCDSRTTYKAKEKGVKLPGYHLVDHCIEILSHDKDYNKVKLYEHAVAHSGLPDN 223
                                    11        21        31        41        51        61  |     71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221  
                                                                                      61  |                                                                                                                                                               
                                                                                         64-CR8                                                                                                                                                           


Chain D from PDB  Type:PROTEIN  Length:221
 aligned with Q5S6Z9_LOBHE | Q5S6Z9 from UniProtKB/TrEMBL  Length:226

    Alignment length:223
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220   
         Q5S6Z9_LOBHE     1 MSAIKPDMKINLRMEGNVNGHHFVIDGDGTGKPFEGKQSMDLEVKEGGPLPFAFDILTTAFHYGNRVFAEYPDHIQDYFKQSFPKGYSWERSLTFEDGGICIARNDITMEGDTFYNKVRFHGVNFPANGPVMQKKTLKWEPSTEKMYVRDGVLTGDITMALLLEGNAHYRCDFRTTYKAKEKGVKLPGYHFVDHCIEILSHDKDYNKVKLYEHAVAHSGLPDN 223
               SCOP domains d3tmtd_ D: automated matches                                                                                                                                                                                                    SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeeeeeeeee..eeeeeeeeeeee....eeeeeeeeee......hhhhhhhhh--...............hhhhh...eeeeeeeee....eeeeeeeeeee..eeeeeeeeeee.....hhhhhh.eeee..eeeeeeee..eeeeeeeeeeee....eeeeeeeeeeee..........eeeeeeeeeeee.....eeeeeeeeeee...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3tmt D   1 MSAIKPDMKINLRMEGNVNGHHFVIDGDGTGKPFEGKQSMDLEVKEGGPLPFAFDILTTAF--hNRVFAEYPDHIQDYFKQSFPKGYSWERSLTFEDGGICIARNDITMEGDTFYNKVRFHGVNFPANGPVMQKKTLKWEPSTEKMYVRDGVLTGDITMALLLEGNAHYRCDSRTTYKAKEKGVKLPGYHLVDHCIEILSHDKDYNKVKLYEHAVAHSGLPDN 223
                                    10        20        30        40        50        60|  |    70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220   
                                                                                       61  |                                                                                                                                                               
                                                                                          64-CR8
   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  (1, 4)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3TMT)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3TMT)

(-) Gene Ontology  (2, 2)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C,D   (Q5S6Z9_LOBHE | Q5S6Z9)
biological process
    GO:0008218    bioluminescence    The production of light by certain enzyme-catalyzed reactions in cells.
    GO:0006091    generation of precursor metabolites and energy    The chemical reactions and pathways resulting in the formation of precursor metabolites, substances from which energy is derived, and any process involved in the liberation of energy from these substances.

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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 4ljb 4ljc 4ljd 4oy4 4r6b 5dtl 5fvf 5fvg 5fvi

(-) Related Entries Specified in the PDB File

1zux 2btj 2vvh 2vvi 2vvj 3tmr