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(-) Description

Title :  ROOM TEMPERATURE STRUCTURE OF IRISFP DETERMINED BY SERIAL FEMTOSECOND CRYSTALLOGRAPHY.
 
Authors :  J. P. Colletier, F. X. Gallat, N. Coquelle, M. Weik
Date :  06 Feb 16  (Deposition) - 06 Apr 16  (Release) - 06 Apr 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.75
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Fluorescent Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Colletier, M. Sliwa, F. Gallat, M. Sugahara, V. Guillon, G. Schiro, N. Coquelle, J. Woodhouse, L. Roux, G. Gotthard, A. Royant, L. M. Uriarte, C. Ruckebusch, Y. Joti, M. Byrdin, E. Mizohata, E. Nango T. Tanaka, K. Tono, M. Yabashi, V. Adam, M. Cammarata, I. Schlichting, D. Bourgeois, M. Weik
Serial Femtosecond Crystallography And Ultrafast Absorption Spectroscopy Of The Photoswitchable Fluorescent Protein Irisfp.
J. Phys. Chem. Lett. V. 7 882 2016
PubMed-ID: 26866390  |  Reference-DOI: 10.1021/ACS.JPCLETT.5B02789

(-) 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
    Organism Common: LOBED BRAIN CORAL
    Organism Scientific: LOBOPHYLLIA HEMPRICHII
    Organism Taxid: 46758
    Synonym: IRISFP, A GREEN TO RED PHOTOCONVERTIBLE GPF-LIKE PROTEIN EOSFP

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 25)

Asymmetric/Biological Unit (3, 25)
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
2NH42Ligand/IonAMMONIUM ION
3SO419Ligand/IonSULFATE ION

(-) Sites  (17, 17)

Asymmetric Unit (17, 17)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASP A:202 , LYS A:203BINDING SITE FOR RESIDUE SO4 A 301
02AC2SOFTWAREARG A:149 , ASP A:150 , HOH A:2069 , ALA D:167BINDING SITE FOR RESIDUE SO4 A 302
03AC3SOFTWAREASN A:17 , HIS A:22 , ARG B:104 , HOH B:2058BINDING SITE FOR RESIDUE SO4 A 304
04AC4SOFTWARELYS A:85BINDING SITE FOR RESIDUE SO4 A 307
05AC5SOFTWAREARG A:119 , HOH A:2056 , ASN B:17 , HIS B:22 , HIS B:121BINDING SITE FOR RESIDUE SO4 B 301
06AC6SOFTWAREGLY B:47BINDING SITE FOR RESIDUE SO4 B 302
07AC7SOFTWAREALA B:167 , HOH B:2076 , ARG C:149 , ASP C:150BINDING SITE FOR RESIDUE SO4 C 301
08AC8SOFTWARELYS A:37 , LYS C:9 , HOH C:2004BINDING SITE FOR RESIDUE SO4 C 302
09AC9SOFTWAREARG C:104 , ARG C:119 , HOH C:2075 , ASN D:17 , HIS D:22 , HIS D:121BINDING SITE FOR RESIDUE SO4 C 303
10BC1SOFTWAREGLY C:47 , HOH C:2011 , HOH C:2022BINDING SITE FOR RESIDUE SO4 C 304
11BC2SOFTWAREASP C:202 , LYS C:203BINDING SITE FOR RESIDUE SO4 C 306
12BC3SOFTWAREASN C:17 , HOH C:2007 , ARG D:119BINDING SITE FOR RESIDUE SO4 D 301
13BC4SOFTWAREHOH A:2074 , ARG D:149 , ASP D:150BINDING SITE FOR RESIDUE SO4 D 302
14BC5SOFTWARELYS D:45 , GLU D:46 , GLY D:47BINDING SITE FOR RESIDUE SO4 D 303
15BC6SOFTWAREASP D:202 , LYS D:203 , HOH D:2086BINDING SITE FOR RESIDUE SO4 D 305
16BC7SOFTWAREPRO D:51BINDING SITE FOR RESIDUE SO4 D 306
17BC8SOFTWAREGLU A:46 , GLY A:47BINDING SITE FOR RESIDUES SO4 A 303 AND NH4 A 306

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5FVF)

(-) 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
7Ser C:2 -Ala C:3
8Gly C:48 -Pro C:49
9Phe C:83 -Pro C:84
10Leu C:220 -Pro C:221
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 5FVF)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5FVF)

(-) Exons   (0, 0)

(no "Exon" information available for 5FVF)

(-) 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:223
                                                                                                                                                                                                                                                               
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........eeeeeeeeeee..eeeeeeeeeeee....eeeeeeeeee......hhhhhhhhh...............hhhhh...eeeeeeeee....eeeeeeeeeee..eeeeeeeeeee............eeee..eeeeeeee..eeeeeeeeeeee...eeeeeeeeeeeee..........eeeeeeeeeeee.....eeeeeeeeeee...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5fvf A  -1 HHMSAIKPDMKINLRMEGNVNGHHFVIDGDGTGKPFEGKQSMDLEVKEGGPLPFAFDILTTAFhNRVFAEYPDHIQDYFKQSFPKGYSWERSLTFEDGGICIARNDITMEGDTFYNKVRFHGVNFPANGPVMQKKTLKWEPSTEKMYVRDGVLTGDITMALLLEGNAHYRCDSRTTYKAKEKGVKLPGYHLVDHCIEILSHDKDYNKVKLYEHAVAHSGLPDN 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 B from PDB  Type:PROTEIN  Length:223
                                                                                                                                                                                                                                                               
               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
                 5fvf B  -1 HHMSAIKPDMKINLRMEGNVNGHHFVIDGDGTGKPFEGKQSMDLEVKEGGPLPFAFDILTTAFhNRVFAEYPDHIQDYFKQSFPKGYSWERSLTFEDGGICIARNDITMEGDTFYNKVRFHGVNFPANGPVMQKKTLKWEPSTEKMYVRDGVLTGDITMALLLEGNAHYRCDSRTTYKAKEKGVKLPGYHLVDHCIEILSHDKDYNKVKLYEHAVAHSGLPDN 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 C from PDB  Type:PROTEIN  Length:221
                                                                                                                                                                                                                                                             
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeeeeeeeee..eeeeeeeeeeee....eeeeeeeeee......hhhhhhhhh...............hhhhh...eeeeeeeee....eeeeeeeeeee..eeeeeeeeeee............eeee..eeeeeeee..eeeeeeeeeeee...eeeeeeeeeeeee..........eeeeeeeeeeee.....eeeeeeeeeee...... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5fvf C   1 MSAIKPDMKINLRMEGNVNGHHFVIDGDGTGKPFEGKQSMDLEVKEGGPLPFAFDILTTAFhNRVFAEYPDHIQDYFKQSFPKGYSWERSLTFEDGGICIARNDITMEGDTFYNKVRFHGVNFPANGPVMQKKTLKWEPSTEKMYVRDGVLTGDITMALLLEGNAHYRCDSRTTYKAKEKGVKLPGYHLVDHCIEILSHDKDYNKVKLYEHAVAHSGLPDN 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 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......hhhhhhhhh.......................eeeeeeeee....eeeeeeeeeee..eeeeeeeeeee............eeee..eeeeeeee..eeeeeeeeeeee....eeeeeeeeeeee..........eeeeeeeeeeee.....eeeeeeeeeee...... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5fvf D   1 MSAIKPDMKINLRMEGNVNGHHFVIDGDGTGKPFEGKQSMDLEVKEGGPLPFAFDILTTAFhNRVFAEYPDHIQDYFKQSFPKGYSWERSLTFEDGGICIARNDITMEGDTFYNKVRFHGVNFPANGPVMQKKTLKWEPSTEKMYVRDGVLTGDITMALLLEGNAHYRCDSRTTYKAKEKGVKLPGYHLVDHCIEILSHDKDYNKVKLYEHAVAHSGLPDN 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 5FVF)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5FVF)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5FVF)

(-) 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 ]  
    Gly B:48 - Pro B:49   [ RasMol ]  
    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 ]  
    Leu C:220 - Pro C:221   [ RasMol ]  
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    Phe A:83 - Pro A:84   [ 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 4r6b 5dtl 5fvg 5fvi

(-) Related Entries Specified in the PDB File

5fvg STRUCTURE OF IRISFP AT 100 K.
5fvi STRUCTURE OF IRISFP IN MINERAL GREASE AT 100 K.