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(-) Description

Title :  FLUORESCENT PROTEIN MKEIMA AT PH 3.8
 
Authors :  S. Violot, P. Carpentier, L. Blanchoin, D. Bourgeois
Date :  06 May 09  (Deposition) - 11 Aug 09  (Release) - 04 Jul 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Biol. Unit 4:  D  (1x)
Keywords :  Fluorescent Protein, Stokes Shift, Mkeima (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  S. Violot, P. Carpentier, L. Blanchoin, D. Bourgeois
Reverse Ph-Dependence Of Chromophore Protonation Explains The Large Stokes Shift Of The Red Fluorescent Protein Mkeima.
J. Am. Chem. Soc. V. 131 10356 2009
PubMed-ID: 19722611  |  Reference-DOI: 10.1021/JA903695N

(-) Compounds

Molecule 1 - LARGE STOKES SHIFT FLUORESCENT PROTEIN
    ChainsA, B, C, D
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET15-B
    Expression System StrainROSETTA(DE3)
    Expression System Taxid562
    Organism ScientificMONTIPORA SP. 20
    Organism Taxid321802

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit ABCD
Biological Unit 1 (1x)A   
Biological Unit 2 (1x) B  
Biological Unit 3 (1x)  C 
Biological Unit 4 (1x)   D

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 15)

Asymmetric Unit (2, 15)
No.NameCountTypeFull Name
1CRQ4Mod. Amino Acid[2-(3-CARBAMOYL-1-IMINO-PROPYL)-4-(4-HYDROXY-BENZYLIDENE)-5-OXO-4,5-DIHYDRO-IMIDAZOL-1-YL]-ACETIC ACID
2SO411Ligand/IonSULFATE ION
Biological Unit 1 (2, 4)
No.NameCountTypeFull Name
1CRQ1Mod. Amino Acid[2-(3-CARBAMOYL-1-IMINO-PROPYL)-4-(4-HYDROXY-BENZYLIDENE)-5-OXO-4,5-DIHYDRO-IMIDAZOL-1-YL]-ACETIC ACID
2SO43Ligand/IonSULFATE ION
Biological Unit 2 (2, 4)
No.NameCountTypeFull Name
1CRQ1Mod. Amino Acid[2-(3-CARBAMOYL-1-IMINO-PROPYL)-4-(4-HYDROXY-BENZYLIDENE)-5-OXO-4,5-DIHYDRO-IMIDAZOL-1-YL]-ACETIC ACID
2SO43Ligand/IonSULFATE ION
Biological Unit 3 (2, 3)
No.NameCountTypeFull Name
1CRQ1Mod. Amino Acid[2-(3-CARBAMOYL-1-IMINO-PROPYL)-4-(4-HYDROXY-BENZYLIDENE)-5-OXO-4,5-DIHYDRO-IMIDAZOL-1-YL]-ACETIC ACID
2SO42Ligand/IonSULFATE ION
Biological Unit 4 (2, 4)
No.NameCountTypeFull Name
1CRQ1Mod. Amino Acid[2-(3-CARBAMOYL-1-IMINO-PROPYL)-4-(4-HYDROXY-BENZYLIDENE)-5-OXO-4,5-DIHYDRO-IMIDAZOL-1-YL]-ACETIC ACID
2SO43Ligand/IonSULFATE ION

(-) Sites  (11, 11)

Asymmetric Unit (11, 11)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREARG D:216 , HIS D:217 , HOH D:2209 , HOH D:2210 , HOH D:2211BINDING SITE FOR RESIDUE SO4 D1222
02AC2SOFTWAREARG B:216 , HIS B:217 , HOH B:2221BINDING SITE FOR RESIDUE SO4 B1222
03AC3SOFTWARETHR D:102 , VAL D:103 , SER D:104 , LYS D:119 , ILE D:120 , SER D:121BINDING SITE FOR RESIDUE SO4 D1223
04AC4SOFTWAREASN C:94 , PHE C:95 , GLU D:96 , HIS D:168 , LEU D:170 , HOH D:2213 , HOH D:2214BINDING SITE FOR RESIDUE SO4 D1224
05AC5SOFTWAREASN A:94 , PHE A:95 , GLU A:96 , GLU A:172 , GLU B:96 , HIS B:168 , LEU B:170BINDING SITE FOR RESIDUE SO4 A1220
06AC6SOFTWAREGLU B:90 , ARG B:91 , SER B:92 , LYS B:174 , THR B:176BINDING SITE FOR RESIDUE SO4 B1223
07AC7SOFTWARETHR B:102 , SER B:104 , LYS B:119 , ILE B:120 , SER B:121BINDING SITE FOR RESIDUE SO4 B1224
08AC8SOFTWARETHR A:102 , VAL A:103 , SER A:104 , LYS A:119 , ILE A:120 , SER A:121BINDING SITE FOR RESIDUE SO4 A1221
09AC9SOFTWARETHR C:102 , VAL C:103 , SER C:104 , LYS C:119 , SER C:121BINDING SITE FOR RESIDUE SO4 C1220
10BC1SOFTWAREGLU A:96 , HIS A:168 , LEU A:170 , ASN B:94 , PHE B:95 , GLU B:96 , HOH B:2120BINDING SITE FOR RESIDUE SO4 A1222
11BC2SOFTWAREVAL C:18 , ASN C:19 , HIS C:21 , PRO C:51BINDING SITE FOR RESIDUE SO4 C1221

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2WHS)

(-) Cis Peptide Bonds  (8, 8)

Asymmetric Unit
No.Residues
1Gly A:48 -Pro A:49
2Phe A:83 -Pro A:84
3Gly B:48 -Pro B:49
4Phe B:83 -Pro B:84
5Gly C:48 -Pro C:49
6Phe C:83 -Pro C:84
7Gly 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 2WHS)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2WHS)

(-) Exons   (0, 0)

(no "Exon" information available for 2WHS)

(-) Sequences/Alignments

Asymmetric 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:217
 aligned with Q1JV70_9CNID | Q1JV70 from UniProtKB/TrEMBL  Length:222

    Alignment length:219
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211         
         Q1JV70_9CNID     2 VSVIAKQMTYKVYMSGTVNGHYFEVEGDGKGKPYEGEQTVKLTVTKGGPLPFAWDILSPQLQYGSIPFTKYPEDIPDYFKQSFPEGYTWERSMNFEDGAVCTVSNDSSIQGNCFIYNVKISGENFPPNGPVMQKKTQGWEPSTERLFARDGMLIGNDYMALKLEGGGHYLCEFKSTYKAKKPVRMPGRHEIDRKLDVTSHNRDYTSVEQCEIAIARHSL 220
               SCOP domains d2whsa_ A: automated matches                                                                                                                                                                                                SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeeeeeeeee..eeeeeeeeeee.....eeeeeeeeee......hhhhhhhhh.--hhhhh.......hhhhhh....eeeeeeeee....eeeeeeeeeee..eeeeeeeeeee............eeee..eeeeeeee..eeeeeeeeeeee....eeeeeeeeeeee.........eeeeeeeeeeee.....eeeeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2whs A   1 VSVIAKQMTYKVYMSGTVNGHYFEVEGDGKGKPYEGEQTVKLTVTKGGPLPFAWDILSPQLq--SIPFTKYPEDIPDYFKQSFPEGYTWERSMNFEDGAVCTVSNDSSIQGNCFIYNVKISGENFPPNGPVMQKKTQGWEPSTERLFARDGMLIGNDYMALKLEGGGHYLCEFKSTYKAKKPVRMPGRHEIDRKLDVTSHNRDYTSVEQCEIAIARHSL 219
                                    10        20        30        40        50        60 |  |   70        80        90       100       110       120       130       140       150       160       170       180       190       200       210         
                                                                                        62-CRQ                                                                                                                                                         

Chain B from PDB  Type:PROTEIN  Length:227
 aligned with Q1JV70_9CNID | Q1JV70 from UniProtKB/TrEMBL  Length:222

    Alignment length:229
                                   1                                                                                                                                                                                                                             
                                   | 3        13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213         
         Q1JV70_9CNID     - -------MVSVIAKQMTYKVYMSGTVNGHYFEVEGDGKGKPYEGEQTVKLTVTKGGPLPFAWDILSPQLQYGSIPFTKYPEDIPDYFKQSFPEGYTWERSMNFEDGAVCTVSNDSSIQGNCFIYNVKISGENFPPNGPVMQKKTQGWEPSTERLFARDGMLIGNDYMALKLEGGGHYLCEFKSTYKAKKPVRMPGRHEIDRKLDVTSHNRDYTSVEQCEIAIARHSLLG 222
               SCOP domains d2whsb_ B: automated matches                                                                                                                                                                                                          SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...............eeeeeeeeeee..eeeeeeeeeeee....eeeeeeeeee......hhhhhhhhh.--hhhhh.......hhhhhh....eeeeeeeee....eeeeeeeeeee..eeeeeeeeeee............eeee..eeeeeeee..eeeeeeeeeeee....eeeeeeeeeeee.........eeeeeeeeeeee.....eeeeeeeeeeee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2whs B  -7 LVPRGSHMVSVIAKQMTYKVYMSGTVNGHYFEVEGDGKGKPYEGEQTVKLTVTKGGPLPFAWDILSPQLq--SIPFTKYPEDIPDYFKQSFPEGYTWERSMNFEDGAVCTVSNDSSIQGNCFIYNVKISGENFPPNGPVMQKKTQGWEPSTERLFARDGMLIGNDYMALKLEGGGHYLCEFKSTYKAKKPVRMPGRHEIDRKLDVTSHNRDYTSVEQCEIAIARHSLLG 221
                                     2        12        22        32        42        52        62  |     72        82        92       102       112       122       132       142       152       162       172       182       192       202       212         
                                                                                                62-CRQ                                                                                                                                                           

Chain C from PDB  Type:PROTEIN  Length:216
 aligned with Q1JV70_9CNID | Q1JV70 from UniProtKB/TrEMBL  Length:222

    Alignment length:218
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212        
         Q1JV70_9CNID     3 SVIAKQMTYKVYMSGTVNGHYFEVEGDGKGKPYEGEQTVKLTVTKGGPLPFAWDILSPQLQYGSIPFTKYPEDIPDYFKQSFPEGYTWERSMNFEDGAVCTVSNDSSIQGNCFIYNVKISGENFPPNGPVMQKKTQGWEPSTERLFARDGMLIGNDYMALKLEGGGHYLCEFKSTYKAKKPVRMPGRHEIDRKLDVTSHNRDYTSVEQCEIAIARHSL 220
               SCOP domains d2whsc_ C: automated matches                                                                                                                                                                                               SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeeeeeeeee..eeeeeeeeeeee....eeeeeeeeee......hhhhhhhhh.--hhhhh.......hhhhhh....eeeeeeeee....eeeeeeeeeee..eeeeeeeeeee............eeee..eeeeeeee..eeeeeeeeeeee....eeeeeeeeeeee.........eeeeeeeeeeee.....eeeeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2whs C   2 SVIAKQMTYKVYMSGTVNGHYFEVEGDGKGKPYEGEQTVKLTVTKGGPLPFAWDILSPQLq--SIPFTKYPEDIPDYFKQSFPEGYTWERSMNFEDGAVCTVSNDSSIQGNCFIYNVKISGENFPPNGPVMQKKTQGWEPSTERLFARDGMLIGNDYMALKLEGGGHYLCEFKSTYKAKKPVRMPGRHEIDRKLDVTSHNRDYTSVEQCEIAIARHSL 219
                                    11        21        31        41        51        61|  |    71        81        91       101       111       121       131       141       151       161       171       181       191       201       211        
                                                                                       62-CRQ                                                                                                                                                         

Chain D from PDB  Type:PROTEIN  Length:227
 aligned with Q1JV70_9CNID | Q1JV70 from UniProtKB/TrEMBL  Length:222

    Alignment length:229
                                   1                                                                                                                                                                                                                             
                                   | 3        13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213         
         Q1JV70_9CNID     - -------MVSVIAKQMTYKVYMSGTVNGHYFEVEGDGKGKPYEGEQTVKLTVTKGGPLPFAWDILSPQLQYGSIPFTKYPEDIPDYFKQSFPEGYTWERSMNFEDGAVCTVSNDSSIQGNCFIYNVKISGENFPPNGPVMQKKTQGWEPSTERLFARDGMLIGNDYMALKLEGGGHYLCEFKSTYKAKKPVRMPGRHEIDRKLDVTSHNRDYTSVEQCEIAIARHSLLG 222
               SCOP domains d2whsd_ D: automated matches                                                                                                                                                                                                          SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) --------GFP-2whsD01 D:1-218                                                                                                                                                                                                       --- Pfam domains (1)
           Pfam domains (2) --------GFP-2whsD02 D:1-218                                                                                                                                                                                                       --- Pfam domains (2)
           Pfam domains (3) --------GFP-2whsD03 D:1-218                                                                                                                                                                                                       --- Pfam domains (3)
           Pfam domains (4) --------GFP-2whsD04 D:1-218                                                                                                                                                                                                       --- Pfam domains (4)
         Sec.struct. author ...............eeeeeeeeeee..eeeeeeeeeeee....eeeeeeeeee......hhhhhhhhh.--hhhhh.......hhhhhh....eeeeeeeee....eeeeeeeeeee..eeeeeeeeeee............eeee..eeeeeeee..eeeeeeeeeeee....eeeeeeeeeeee.........eeeeeeeeeeee.....eeeeeeeeeeee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2whs D  -7 LVPRGSHMVSVIAKQMTYKVYMSGTVNGHYFEVEGDGKGKPYEGEQTVKLTVTKGGPLPFAWDILSPQLq--SIPFTKYPEDIPDYFKQSFPEGYTWERSMNFEDGAVCTVSNDSSIQGNCFIYNVKISGENFPPNGPVMQKKTQGWEPSTERLFARDGMLIGNDYMALKLEGGGHYLCEFKSTYKAKKPVRMPGRHEIDRKLDVTSHNRDYTSVEQCEIAIARHSLLG 221
                                     2        12        22        32        42        52        62  |     72        82        92       102       112       122       132       142       152       162       172       182       192       202       212         
                                                                                                62-CRQ                                                                                                                                                           

   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  (1, 4)

Asymmetric Unit

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2WHS)

(-) Pfam Domains  (1, 4)

Asymmetric Unit
(-)
Clan: GFP (101)
(-)
Family: GFP (101)
1aGFP-2whsD01D:1-218
1bGFP-2whsD02D:1-218
1cGFP-2whsD03D:1-218
1dGFP-2whsD04D:1-218

(-) Gene Ontology  (1, 1)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (Q1JV70_9CNID | Q1JV70)
biological process
    GO:0008218    bioluminescence    The production of light by certain enzyme-catalyzed reactions in cells.

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 Related Entries

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

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        Q1JV70_9CNID | Q1JV702wht 2whu 3ir8

(-) Related Entries Specified in the PDB File

2wht FLUORESCENT PROTEIN MKEIMA AT PH 5.6
2whu FLUORESCENT PROTEIN MKEIMA AT PH 8.0