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(-) Description

Title :  IRISFP, PLANAR 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  (3, 27)

Asymmetric/Biological Unit (3, 27)
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
3SO419Ligand/IonSULFATE ION

(-) Sites  (23, 23)

Asymmetric Unit (23, 23)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASN A:17 , HIS A:22 , HIS A:121 , HOH A:369 , HOH A:867 , HOH B:623 , HOH B:1031BINDING SITE FOR RESIDUE SO4 A 1224
02AC2SOFTWAREASP A:202 , LYS A:203 , HOH A:1100BINDING SITE FOR RESIDUE SO4 A 1225
03AC3SOFTWAREASN A:11 , LEU A:12 , ARG A:13 , ASP A:26BINDING SITE FOR RESIDUE SO4 A 227
04AC4SOFTWARECYS A:195 , ILE A:196 , GLU A:197 , TYR A:211 , HIS A:213BINDING SITE FOR RESIDUE SO3 A 228
05AC5SOFTWAREHOH A:1077 , ASN B:17 , HIS B:22 , HIS B:121 , HOH B:242 , HOH B:850BINDING SITE FOR RESIDUE SO4 B 1224
06AC6SOFTWAREASP B:202 , LYS B:203 , HOH B:989BINDING SITE FOR RESIDUE SO4 B 1225
07AC7SOFTWAREARG B:149 , ASP B:150 , HOH B:239 , HOH B:267 , HOH B:273 , HOH B:874 , HOH B:1055 , HOH B:1092 , ALA D:167BINDING SITE FOR RESIDUE SO4 B 227
08AC8SOFTWARELYS B:45 , GLU B:46 , GLY B:47 , HOH B:1217BINDING SITE FOR RESIDUE SO4 B 228
09AC9SOFTWARECYS B:195 , ILE B:196 , TYR B:211 , GLU B:212 , HIS B:213 , HOH B:1054 , HOH B:1229BINDING SITE FOR RESIDUE SO3 B 229
10BC1SOFTWARELYS B:182 , GLY B:183 , HOH B:900 , HOH B:1175BINDING SITE FOR RESIDUE SO4 B 230
11BC2SOFTWARETYR A:78 , GLY A:151 , VAL A:184 , LEU A:186 , HOH A:382 , HOH A:614 , HOH A:661 , GLU B:70 , HOH B:552 , HOH B:1260BINDING SITE FOR RESIDUE SO4 B 231
12BC3SOFTWAREALA A:167 , HOH A:1024 , VAL C:148 , ARG C:149 , ASP C:150 , HOH C:231 , HOH C:470BINDING SITE FOR RESIDUE SO4 C 1224
13BC4SOFTWAREASN C:17 , HIS C:22 , HIS C:121 , HOH C:839 , HOH C:1113 , HOH C:1118 , ARG D:119BINDING SITE FOR RESIDUE SO4 C 1225
14BC5SOFTWAREASP C:202 , LYS C:203BINDING SITE FOR RESIDUE SO4 C 1226
15BC6SOFTWARELYS C:182 , GLY C:183 , HOH C:971 , HOH C:1120BINDING SITE FOR RESIDUE SO4 C 1227
16BC7SOFTWARELYS C:45 , GLU C:46 , GLY C:47 , HOH C:512BINDING SITE FOR RESIDUE SO4 C 227
17BC8SOFTWARECYS C:195 , ILE C:196 , GLU C:197 , TYR C:211 , GLU C:212 , HIS C:213 , HOH C:250BINDING SITE FOR RESIDUE SO3 C 228
18BC9SOFTWAREASN D:17 , HIS D:22 , HIS D:121 , HOH D:286 , HOH D:846 , HOH D:860BINDING SITE FOR RESIDUE SO4 D 1225
19CC1SOFTWAREASP D:202 , LYS D:203 , HOH D:1124BINDING SITE FOR RESIDUE SO4 D 1226
20CC2SOFTWARELYS D:182 , GLY D:183BINDING SITE FOR RESIDUE SO4 D 1227
21CC3SOFTWAREGLU D:46 , GLY D:47 , HOH D:944BINDING SITE FOR RESIDUE SO4 D 227
22CC4SOFTWAREALA B:167 , ARG D:149 , ASP D:150 , HOH D:245 , HOH D:380 , HOH D:907 , HOH D:911BINDING SITE FOR RESIDUE SO4 D 228
23CC5SOFTWARECYS D:195 , ILE D:196 , GLU D:197 , TYR D:211 , GLU D:212 , HIS D:213BINDING SITE FOR RESIDUE SO3 D 229

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (13, 13)

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
10Met D:1 -Ser D:2
11Gly D:48 -Pro D:49
12Phe D:83 -Pro D:84
13Leu D:220 -Pro D:221

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3TMR)

(-) 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 d3tmra_ A: automated matches                                                                                                                                                                                                     SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eeeeeeeeeee..eeeeeeeeeeee....eeeeeeeeee......hhhhhhhhh--...............hhhhh...eeeeeeeee....eeeeeeeeeee..eeeeeeeeeee............eeee..eeeeeeee..eeeeeeeeeeee....eeeeeeeeeeee..........eeeeeeeeeeee.....eeeeeeeeeee...... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3tmr 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 d3tmrb_ B: automated matches                                                                                                                                                                                                    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
                 3tmr 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: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 d3tmrc_ C: automated matches                                                                                                                                                                                                    SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeeeeeeeee..eeeeeeeeeeee....eeeeeeeeee......hhhhhhhhh--...............hhhhh...eeeeeeeee....eeeeeeeeeee..eeeeeeeeeee............eeee..eeeeeeee..eeeeeeeeeeee....eeeeeeeeeeee..........eeeeeeeeeeee.....eeeeeeeeeee...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3tmr C   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 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 d3tmrd_ D: automated matches                                                                                                                                                                                                    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
                 3tmr 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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    → 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  (1, 4)

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

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) 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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  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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    Leu D:220 - Pro D: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 3tmt 4ljb 4ljc 4ljd 4oy4 4r6b 5dtl 5fvf 5fvg 5fvi

(-) Related Entries Specified in the PDB File

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