2H8Q - JenaLib

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Title :   CRYSTAL STRUCTURE OF A REDSHIFTED MUTANT (K83M) OF THE RED FLUORESCENT PROTEIN DRFP583/DSRED

Authors :   C. A. Yarbrough, S. J. Remington

Date :   07 Jun 06 (Deposition) - 22 Aug 06 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.00

Chains :   Asym. Unit : A,B,C,D
Biol. Unit 1: A,B  (2x)
Biol. Unit 2: C,D  (2x)

Keywords :   Beta Barrel, Fluorescent, Red Shift, Gfp, Dsred, Bioluminescence, Luminescent Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   X. Shu, N. C. Shaner, C. A. Yarbrough, R. Y. Tsien, S. J. Remington
Novel Chromophores And Buried Charges Control Color In Mfruits(, ).
Biochemistry V. 45 9639 2006
PubMed-ID: 16893165 | Reference-DOI: 10.1021/BI060773L

Molecule 1 - RED FLUORESCENT PROTEIN DRFP583
	Chains	:	A, B, C, D
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PQE-30
	Expression System Strain	:	JM-109
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	DRFP583
	Mutation	:	YES
	Organism Scientific	:	DISCOSOMA SP.
	Organism Taxid	:	86600
	Synonym	:	DSRED

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 4)

No.	Name	Count	Type	Full Name
1	CRQ	4	Mod. Amino Acid	[2-(3-CARBAMOYL-1-IMINO-PROPYL)-4-(4-HYDROXY-BENZYLIDENE)-5-OXO-4,5-DIHYDRO-IMIDAZOL-1-YL]-ACETICACID

Biological Unit 1 (1, 4)

No.	Name	Count	Type	Full Name
1	CRQ	4	Mod. Amino Acid	[2-(3-CARBAMOYL-1-IMINO-PROPYL)-4-(4-HYDROXY-BENZYLIDENE)-5-OXO-4,5-DIHYDRO-IMIDAZOL-1-YL]-ACETICACID

Biological Unit 2 (1, 4)

No.	Name	Count	Type	Full Name
1	CRQ	4	Mod. Amino Acid	[2-(3-CARBAMOYL-1-IMINO-PROPYL)-4-(4-HYDROXY-BENZYLIDENE)-5-OXO-4,5-DIHYDRO-IMIDAZOL-1-YL]-ACETICACID

(no "Site" information available for 2H8Q)

(no "SS Bond" information available for 2H8Q)

Asymmetric Unit

No.	Residues
1	Gly A:52	-	Pro A:53
2	Phe A:87	-	Pro A:88
3	Gly B:52	-	Pro B:53
4	Phe B:87	-	Pro B:88
5	Gly C:52	-	Pro C:53
6	Phe C:87	-	Pro C:88
7	Gly D:52	-	Pro D:53
8	Phe D:87	-	Pro D:88

(no "SAP(SNP)/Variant" information available for 2H8Q)

(no "PROSITE Motif" information available for 2H8Q)

(no "Exon" information available for 2H8Q)

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 RFP_DISSP | Q9U6Y8 from UniProtKB/Swiss-Prot  Length:225

    Alignment length:219
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216         
            RFP_DISSP     7 VIKEFMRFKVRMEGTVNGHEFEIEGEGEGRPYEGHNTVKLKVTKGGPLPFAWDILSPQFQYGSKVYVKHPADIPDYKKLSFPEGFKWERVMNFEDGGVVTVTQDSSLQDGCFIYKVKFIGVNFPSDGPVMQKKTMGWEASTERLYPRDGVLKGEIHKALKLKDGGHYLVEFKSIYMAKKPVQLPGYYYVDSKLDITSHNEDYTIVEQYERTEGRHHLFL 225
               SCOP domains d2h8qa_ A: Red fluorescent protein (fp583 or dsred(clontech)  )                                                                                                                                                             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.....eeeeeeeeeee..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2h8q A   7 VIKEFMRFKVRMEGTVNGHEFEIEGEGEGRPYEGHNTVKLKVTKGGPLPFAWDILSPQFq--SKVYVKHPADIPDYMKLSFPEGFKWERVMNFEDGGVVTVTQDSSLQDGCFIYKVKFIGVNFPSDGPVMQKKTMGWEASTERLYPRDGVLKGEIHKALKLKDGGHYLVEFKSIYMAKKPVQLPGYYYVDSKLDITSHNEDYTIVEQYERTEGRHHLFL 225
                                    16        26        36        46        56        66  |     76        86        96       106       116       126       136       146       156       166       176       186       196       206       216         
                                                                                      66-CRQ

Chain B from PDB  Type:PROTEIN  Length:217
 aligned with RFP_DISSP | Q9U6Y8 from UniProtKB/Swiss-Prot  Length:225

    Alignment length:219
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216         
            RFP_DISSP     7 VIKEFMRFKVRMEGTVNGHEFEIEGEGEGRPYEGHNTVKLKVTKGGPLPFAWDILSPQFQYGSKVYVKHPADIPDYKKLSFPEGFKWERVMNFEDGGVVTVTQDSSLQDGCFIYKVKFIGVNFPSDGPVMQKKTMGWEASTERLYPRDGVLKGEIHKALKLKDGGHYLVEFKSIYMAKKPVQLPGYYYVDSKLDITSHNEDYTIVEQYERTEGRHHLFL 225
               SCOP domains d2h8qb_ B: Red fluorescent protein (fp583 or dsred(clontech)  )                                                                                                                                                             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.....eeeeeeeeeee..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2h8q B   7 VIKEFMRFKVRMEGTVNGHEFEIEGEGEGRPYEGHNTVKLKVTKGGPLPFAWDILSPQFq--SKVYVKHPADIPDYMKLSFPEGFKWERVMNFEDGGVVTVTQDSSLQDGCFIYKVKFIGVNFPSDGPVMQKKTMGWEASTERLYPRDGVLKGEIHKALKLKDGGHYLVEFKSIYMAKKPVQLPGYYYVDSKLDITSHNEDYTIVEQYERTEGRHHLFL 225
                                    16        26        36        46        56        66  |     76        86        96       106       116       126       136       146       156       166       176       186       196       206       216         
                                                                                      66-CRQ

Chain C from PDB  Type:PROTEIN  Length:217
 aligned with RFP_DISSP | Q9U6Y8 from UniProtKB/Swiss-Prot  Length:225

    Alignment length:219
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216         
            RFP_DISSP     7 VIKEFMRFKVRMEGTVNGHEFEIEGEGEGRPYEGHNTVKLKVTKGGPLPFAWDILSPQFQYGSKVYVKHPADIPDYKKLSFPEGFKWERVMNFEDGGVVTVTQDSSLQDGCFIYKVKFIGVNFPSDGPVMQKKTMGWEASTERLYPRDGVLKGEIHKALKLKDGGHYLVEFKSIYMAKKPVQLPGYYYVDSKLDITSHNEDYTIVEQYERTEGRHHLFL 225
               SCOP domains d2h8qc_ C: Red fluorescent protein (fp583 or dsred(clontech)  )                                                                                                                                                             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.....eeeeeeeeeee..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2h8q C   7 VIKEFMRFKVRMEGTVNGHEFEIEGEGEGRPYEGHNTVKLKVTKGGPLPFAWDILSPQFq--SKVYVKHPADIPDYMKLSFPEGFKWERVMNFEDGGVVTVTQDSSLQDGCFIYKVKFIGVNFPSDGPVMQKKTMGWEASTERLYPRDGVLKGEIHKALKLKDGGHYLVEFKSIYMAKKPVQLPGYYYVDSKLDITSHNEDYTIVEQYERTEGRHHLFL 225
                                    16        26        36        46        56        66  |     76        86        96       106       116       126       136       146       156       166       176       186       196       206       216         
                                                                                      66-CRQ

Chain D from PDB  Type:PROTEIN  Length:217
 aligned with RFP_DISSP | Q9U6Y8 from UniProtKB/Swiss-Prot  Length:225

    Alignment length:219
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216         
            RFP_DISSP     7 VIKEFMRFKVRMEGTVNGHEFEIEGEGEGRPYEGHNTVKLKVTKGGPLPFAWDILSPQFQYGSKVYVKHPADIPDYKKLSFPEGFKWERVMNFEDGGVVTVTQDSSLQDGCFIYKVKFIGVNFPSDGPVMQKKTMGWEASTERLYPRDGVLKGEIHKALKLKDGGHYLVEFKSIYMAKKPVQLPGYYYVDSKLDITSHNEDYTIVEQYERTEGRHHLFL 225
               SCOP domains d2h8qd_ D: Red fluorescent protein (fp583 or dsred(clontech)  )                                                                                                                                                             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.....eeeeeeeeeee..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2h8q D   7 VIKEFMRFKVRMEGTVNGHEFEIEGEGEGRPYEGHNTVKLKVTKGGPLPFAWDILSPQFq--SKVYVKHPADIPDYMKLSFPEGFKWERVMNFEDGGVVTVTQDSSLQDGCFIYKVKFIGVNFPSDGPVMQKKTMGWEASTERLYPRDGVLKGEIHKALKLKDGGHYLVEFKSIYMAKKPVQLPGYYYVDSKLDITSHNEDYTIVEQYERTEGRHHLFL 225
                                    16        26        36        46        56        66  |     76        86        96       106       116       126       136       146       156       166       176       186       196       206       216         
                                                                                      66-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 '\|'

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: Fluorescent proteins (271)

Protein domain: Red fluorescent protein (fp583 or dsred(clontech)) (3)

Coral (Discosoma sp.) [TaxId: 86600] (3)

1a	d2h8qa_	A:
1b	d2h8qc_	C:
1c	d2h8qd_	D:
1d	d2h8qb_	B:

(no "CATH Domain" information available for 2H8Q)

(no "Pfam Domain" information available for 2H8Q)

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D (RFP_DISSP | Q9U6Y8)


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.
GO:0018298	protein-chromophore linkage	The covalent or noncovalent attachment of a chromophore to a protein.

Asymmetric Unit
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	Ligands, Modified Residues, Ions
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	Sites
(no "Sites" information available for 2h8q)

	Cis Peptide Bonds
		Gly A:52 - Pro A:53	[ RasMol ]
		Gly B:52 - Pro B:53	[ RasMol ]
		Gly C:52 - Pro C:53	[ RasMol ]
		Gly D:52 - Pro D:53	[ RasMol ]
		Phe A:87 - Pro A:88	[ RasMol ]
		Phe B:87 - Pro B:88	[ RasMol ]
		Phe C:87 - Pro C:88	[ RasMol ]
		Phe D:87 - Pro D:88	[ RasMol ]

Biological Units
	Complete Structure
		Biological Unit 1	[ Jena3D ]
		Biological Unit 2	[ Jena3D ]

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	2h8q
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UniProtKB/Swiss-Prot
	RFP_DISSP \| Q9U6Y8	:	1g7k 1ggx 1zgo 1zgp 1zgq 2h5o 2h5r 2v4e 2vad 2vae 4i2y 4kf4 4kf5

1g7k	CRYSTAL STRUCTURE OF DSRED, A RED FLUORESCENT PROTEIN FROM DISCOSOMA SP.
2h5o	CRYSTAL STRUCTURE OF MORANGE
2h5p	CRYSTAL STRUCTURE OF MSTRAWBERRY AT PH 9.5
2h5q	CRYSTAL STRUCTURE OF MCHERRY
2h5r	CRYSTAL STRUCTURE OF MSTRAWBERRY AT PH 10.5

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 4)

Sites (0, 0)

SS Bonds (0, 0)

Cis Peptide Bonds (8, 8)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

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SCOP Domains (1, 4)

CATH Domains (0, 0)

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Gene Ontology (3, 3)

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Related Entries Specified in the PDB File