3MGF - JenaLib

Asymmetric Unit (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Biological Unit 3 (Jmol Viewer)

Biological Unit 4 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF MONOMERIC KUSABIRA-ORANGE (MKO), ORANGE-EMITTING GFP-LIKE PROTEIN, AT PH 7.5

Authors :   T. Ebisawa, A. Yamamura, J. Ohtsuka, Y. Kameda, K. Hayakawa, K. Nagata, M. Tanokura

Date :   06 Apr 10 (Deposition) - 16 Mar 11 (Release) - 16 Mar 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.80

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 (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   T. Ebisawa, A. Yamamura, J. Ohtsuka, Y. Kameda, K. Hayakawa, K. Nagata M. Tanokura
Crystal Structure Of Monomeric Kusabira-Orange (Mko), Orange-Emitting Gfp-Like Protein, At Ph 7. 5
To Be Published
PubMed: search

Molecule 1 - FLUORESCENT PROTEIN
	Chains	:	A, B, C, D
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	MODIFIED PET-28(+)
	Expression System Strain	:	KRX
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	MKO
	Organism Scientific	:	VERRILLOFUNGIA CONCINNA
	Organism Taxid	:	496660
	Synonym	:	ORANGE-EMITTING GFP-LIKE PROTEIN

		1	2	3	4
Asymmetric Unit	:	A	B	C	D
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)

Asymmetric Unit (1, 4)

No.	Name	Count	Type	Full Name
1	CFY	4	Mod. Amino Acid	[(2S)-2-{(2R)-2-[(1S)-1-AMINO-2-PHENYLETHYL]-2-HYDROXY-2,5-DIHYDRO-1,3-THIAZOL-4-YL}-4-(4-HYDROXYBENZYL)-5-OXO-2,5-DIHYDRO-1H-IMIDAZOL-1-YL]ACETIC ACID

Biological Unit 1 (1, 1)

No.	Name	Count	Type	Full Name
1	CFY	1	Mod. Amino Acid	[(2S)-2-{(2R)-2-[(1S)-1-AMINO-2-PHENYLETHYL]-2-HYDROXY-2,5-DIHYDRO-1,3-THIAZOL-4-YL}-4-(4-HYDROXYBENZYL)-5-OXO-2,5-DIHYDRO-1H-IMIDAZOL-1-YL]ACETIC ACID

Biological Unit 2 (1, 1)

No.	Name	Count	Type	Full Name
1	CFY	1	Mod. Amino Acid	[(2S)-2-{(2R)-2-[(1S)-1-AMINO-2-PHENYLETHYL]-2-HYDROXY-2,5-DIHYDRO-1,3-THIAZOL-4-YL}-4-(4-HYDROXYBENZYL)-5-OXO-2,5-DIHYDRO-1H-IMIDAZOL-1-YL]ACETIC ACID

Biological Unit 3 (1, 1)

No.	Name	Count	Type	Full Name
1	CFY	1	Mod. Amino Acid	[(2S)-2-{(2R)-2-[(1S)-1-AMINO-2-PHENYLETHYL]-2-HYDROXY-2,5-DIHYDRO-1,3-THIAZOL-4-YL}-4-(4-HYDROXYBENZYL)-5-OXO-2,5-DIHYDRO-1H-IMIDAZOL-1-YL]ACETIC ACID

Biological Unit 4 (1, 1)

No.	Name	Count	Type	Full Name
1	CFY	1	Mod. Amino Acid	[(2S)-2-{(2R)-2-[(1S)-1-AMINO-2-PHENYLETHYL]-2-HYDROXY-2,5-DIHYDRO-1,3-THIAZOL-4-YL}-4-(4-HYDROXYBENZYL)-5-OXO-2,5-DIHYDRO-1H-IMIDAZOL-1-YL]ACETIC ACID

(no "Site" information available for 3MGF)

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

Asymmetric Unit

No.	Residues
1	Phe A:86	-	Pro A:87
2	Phe B:86	-	Pro B:87
3	Phe C:86	-	Pro C:87
4	Phe D:86	-	Pro D:87

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

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

(no "Exon" information available for 3MGF)

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:213
 aligned with Q6I7B2_FUNCO | Q6I7B2 from UniProtKB/TrEMBL  Length:218

    Alignment length:216
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212      
         Q6I7B2_FUNCO     3 SVIKPEMKMRYYMDGSVNGHEFTIEGEGTGRPYEGHQEMTLRVTMAKGGPMPFAFDLVSHVFCYGHRPFTKYPEEIPDYFKQAFPEGLSWERSLEFEDGGSASVSAHISLRGNTFYHKSKFTGVNFPADGPIMQNQSVDWEPSTEKITASDGVLKGDVTMYLKLEGGGNHKCQFKTTYKAAKKILKMPGSHYISHRLVRKTEGNITELVEDAVAHS 218
               SCOP domains d3mgfa_ A: automated matches                                                                                                                                                                                             SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ......eeeeeeeeeee..eeeeeeeeeeeehhh.eeeeeeeeee.........hhhhhh.--.-............hhhhhh....eeeeeeeee....eeeeeeeeeee..eeeeeeeeeee............eeee..eeeeeeee..eeeeeeeeeeee....eeeeeeeeeeee..........eeeeeeeeeeee..eeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3mgf A   3 SVIKPEMKMRYYMDGSVNGHEFTIEGEGTGRPYEGHQEMTLRVTMAKGGPMPFAFDLVSHV--f-HRPFTKYPEEIPDYFKQAFPEGLSWERSLEFEDGGSASVSAHISLRGNTFYHKSKFTGVNFPADGPIMQNQSVDWEPSTEKITASDGVLKGDVTMYLKLEGGGNHKCQFKTTYKAAKKILKMPGSHYISHRLVRKTEGNITELVEDAVAHS 218
                                    12        22        32        42        52        62|  | |  72        82        92       102       112       122       132       142       152       162       172       182       192       202       212      
                                                                                       63  | |                                                                                                                                                      
                                                                                          66-CFY                                                                                                                                                    
                                                                                            68

Chain B from PDB  Type:PROTEIN  Length:210
 aligned with Q6I7B2_FUNCO | Q6I7B2 from UniProtKB/TrEMBL  Length:218

    Alignment length:216
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212      
         Q6I7B2_FUNCO     3 SVIKPEMKMRYYMDGSVNGHEFTIEGEGTGRPYEGHQEMTLRVTMAKGGPMPFAFDLVSHVFCYGHRPFTKYPEEIPDYFKQAFPEGLSWERSLEFEDGGSASVSAHISLRGNTFYHKSKFTGVNFPADGPIMQNQSVDWEPSTEKITASDGVLKGDVTMYLKLEGGGNHKCQFKTTYKAAKKILKMPGSHYISHRLVRKTEGNITELVEDAVAHS 218
               SCOP domains d3mgfb_ B: automated matches                                                                                                                                                                                             SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ......eeeeeeeeeee..eeeeeeeeeeeehhh.eeeeeeeeee.........hhhhhh.--.-............hhhhhh....eeeeeeeee....eeeeeeeeeee..eeeeeeeeeee............eeee..eeeeeee....eeeeeeeeeee....eeeeeeeeeeee..---.....eeeeeeeeeeee..eeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3mgf B   3 SVIKPEMKMRYYMDGSVNGHEFTIEGEGTGRPYEGHQEMTLRVTMAKGGPMPFAFDLVSHV--f-HRPFTKYPEEIPDYFKQAFPEGLSWERSLEFEDGGSASVSAHISLRGNTFYHKSKFTGVNFPADGPIMQNQSVDWEPSTEKITASDGVLKGDVTMYLKLEGGGNHKCQFKTTYKAAK---KMPGSHYISHRLVRKTEGNITELVEDAVAHS 218
                                    12        22        32        42        52        62|  | |  72        82        92       102       112       122       132       142       152       162       172       182 |   | 192       202       212      
                                                                                       63  | |                                                                                                                 184 188                              
                                                                                          66-CFY                                                                                                                                                    
                                                                                            68

Chain C from PDB  Type:PROTEIN  Length:213
 aligned with Q6I7B2_FUNCO | Q6I7B2 from UniProtKB/TrEMBL  Length:218

    Alignment length:216
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212      
         Q6I7B2_FUNCO     3 SVIKPEMKMRYYMDGSVNGHEFTIEGEGTGRPYEGHQEMTLRVTMAKGGPMPFAFDLVSHVFCYGHRPFTKYPEEIPDYFKQAFPEGLSWERSLEFEDGGSASVSAHISLRGNTFYHKSKFTGVNFPADGPIMQNQSVDWEPSTEKITASDGVLKGDVTMYLKLEGGGNHKCQFKTTYKAAKKILKMPGSHYISHRLVRKTEGNITELVEDAVAHS 218
               SCOP domains d3mgfc_ C: automated matches                                                                                                                                                                                             SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ......eeeeeeeeeee..eeeeeeeeeeeehhh.eeeeeeeeee.........hhhhhh.--.-............hhhhhh....eeeeeeeee....eeeeeeeeeee..eeeeeeeeeee............eeee..eeeeeee....eeeeeeeeeee....eeeeeeeeeeee..........eeeeeeeeeeee..eeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3mgf C   3 SVIKPEMKMRYYMDGSVNGHEFTIEGEGTGRPYEGHQEMTLRVTMAKGGPMPFAFDLVSHV--f-HRPFTKYPEEIPDYFKQAFPEGLSWERSLEFEDGGSASVSAHISLRGNTFYHKSKFTGVNFPADGPIMQNQSVDWEPSTEKITASDGVLKGDVTMYLKLEGGGNHKCQFKTTYKAAKKILKMPGSHYISHRLVRKTEGNITELVEDAVAHS 218
                                    12        22        32        42        52        62|  | |  72        82        92       102       112       122       132       142       152       162       172       182       192       202       212      
                                                                                       63  | |                                                                                                                                                      
                                                                                          66-CFY                                                                                                                                                    
                                                                                            68

Chain D from PDB  Type:PROTEIN  Length:213
 aligned with Q6I7B2_FUNCO | Q6I7B2 from UniProtKB/TrEMBL  Length:218

    Alignment length:216
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212      
         Q6I7B2_FUNCO     3 SVIKPEMKMRYYMDGSVNGHEFTIEGEGTGRPYEGHQEMTLRVTMAKGGPMPFAFDLVSHVFCYGHRPFTKYPEEIPDYFKQAFPEGLSWERSLEFEDGGSASVSAHISLRGNTFYHKSKFTGVNFPADGPIMQNQSVDWEPSTEKITASDGVLKGDVTMYLKLEGGGNHKCQFKTTYKAAKKILKMPGSHYISHRLVRKTEGNITELVEDAVAHS 218
               SCOP domains d3mgfd_ D: automated matches                                                                                                                                                                                             SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
           Pfam domains (1) GFP-3mgfD01 D:3-218                                                                                                                                                                                                      Pfam domains (1)
           Pfam domains (2) GFP-3mgfD02 D:3-218                                                                                                                                                                                                      Pfam domains (2)
           Pfam domains (3) GFP-3mgfD03 D:3-218                                                                                                                                                                                                      Pfam domains (3)
           Pfam domains (4) GFP-3mgfD04 D:3-218                                                                                                                                                                                                      Pfam domains (4)
         Sec.struct. author ......eeeeeeeeeee..eeeeeeeeeeeehhh.eeeeeeeeee.........hhhhhh.--.-............hhhhhh....eeeeeeeee....eeeeeeeeeee..eeeeeeeeeee............eeee..eeeeeee....eeeeeeeeeee....eeeeeeeeeeee..........eeeeeeeeeeee..eeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3mgf D   3 SVIKPEMKMRYYMDGSVNGHEFTIEGEGTGRPYEGHQEMTLRVTMAKGGPMPFAFDLVSHV--f-HRPFTKYPEEIPDYFKQAFPEGLSWERSLEFEDGGSASVSAHISLRGNTFYHKSKFTGVNFPADGPIMQNQSVDWEPSTEKITASDGVLKGDVTMYLKLEGGGNHKCQFKTTYKAAKKILKMPGSHYISHRLVRKTEGNITELVEDAVAHS 218
                                    12        22        32        42        52        62|  | |  72        82        92       102       112       122       132       142       152       162       172       182       192       202       212      
                                                                                       63  | |                                                                                                                                                      
                                                                                          66-CFY                                                                                                                                                    
                                                                                            68

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 '\|'

Asymmetric Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: Alpha and beta proteins (a+b) (23004)

Fold: GFP-like (339)

Superfamily: GFP-like (339)

Family: automated matches (66)

Protein domain: automated matches (66)

Verrillofungia concinna [TaxId: 496660] (1)

1a	d3mgfa_	A:
1b	d3mgfb_	B:
1c	d3mgfc_	C:
1d	d3mgfd_	D:

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

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: GFP (101)

Family: GFP (101)

Fungia concinna (Mushroom coral) (Verrillofungia concinna) (3)

1a	GFP-3mgfD01	D:3-218
1b	GFP-3mgfD02	D:3-218
1c	GFP-3mgfD03	D:3-218
1d	GFP-3mgfD04	D:3-218

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D (Q6I7B2_FUNCO | Q6I7B2)

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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	Sites
(no "Sites" information available for 3mgf)

	Cis Peptide Bonds
		Phe A:86 - Pro A:87	[ RasMol ]
		Phe B:86 - Pro B:87	[ RasMol ]
		Phe C:86 - Pro C:87	[ RasMol ]
		Phe D:86 - Pro D:87	[ RasMol ]

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(no "Related Entries Specified in the PDB File" available for 3MGF)

Description

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Ligands, Modified Residues, Ions (1, 4)

Sites (0, 0)

SS Bonds (0, 0)

Cis Peptide Bonds (4, 4)

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