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Title :   CRYSTAL STRUCTURE OF WILD TYPE YELLOW FLUORESCENT PROTEIN ZFP538 FROM ZOANTHUS

Authors :   S. J. Remington, R. M. Wachter, D. K. Yarbrough, B. Branchaud, D. C. Anderson, K. Kallio, K. A. Lukyanov

Date :   25 Aug 04 (Deposition) - 08 Feb 05 (Release) - 30 Jun 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.70

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

Keywords :   Fluorescent Protein, Beta-Can, Beta-Barrel, Luminescent Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. J. Remington, R. M. Wachter, D. K. Yarbrough, B. Branchaud, D. C. Anderson, K. Kallio, K. A. Lukyanov
Zfp538, A Yellow-Fluorescent Protein From Zoanthus, Contains A Novel Three-Ring Chromophore.
Biochemistry V. 44 202 2005
PubMed-ID: 15628861 | Reference-DOI: 10.1021/BI048383R
(for further references see the PDB file header)

Molecule 1 - FLUORESCENT PROTEIN FP538
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PQE-30
	Expression System Strain	:	JM-109(DE3)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Mutation	:	YES
	Organism Scientific	:	ZOANTHUS SP.
	Organism Taxid	:	105402

		1	2
Asymmetric Unit	:	A	B
Biological Unit 1 (2x)	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (4, 10)

No.	Name	Count	Type	Full Name
1	BME	2	Ligand/Ion	BETA-MERCAPTOETHANOL
2	CH7	2	Mod. Amino Acid	[(4Z)-4-(4-HYDROXYBENZYLIDENE)-5-OXO-2-(3,4,5,6-TETRAHYDROPYRIDIN-2-YL)-4,5-DIHYDRO-1H-IMIDAZOL-1-YL]ACETIC ACID
3	CSO	4	Mod. Amino Acid	S-HYDROXYCYSTEINE
4	NFA	2	Mod. Amino Acid	PHENYLALANINE AMIDE

Biological Unit 1 (4, 20)

No.	Name	Count	Type	Full Name
1	BME	4	Ligand/Ion	BETA-MERCAPTOETHANOL
2	CH7	4	Mod. Amino Acid	[(4Z)-4-(4-HYDROXYBENZYLIDENE)-5-OXO-2-(3,4,5,6-TETRAHYDROPYRIDIN-2-YL)-4,5-DIHYDRO-1H-IMIDAZOL-1-YL]ACETIC ACID
3	CSO	8	Mod. Amino Acid	S-HYDROXYCYSTEINE
4	NFA	4	Mod. Amino Acid	PHENYLALANINE AMIDE

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HIS A:6 , GLY A:7 , CYS A:87 , VAL A:113	BINDING SITE FOR RESIDUE BME A 587
2	AC2	SOFTWARE	HIS B:6 , LEU B:8 , CYS B:87 , VAL B:113 , VAL B:115	BINDING SITE FOR RESIDUE BME B 587

(no "SS Bond" information available for 1XAE)

Asymmetric Unit

No.	Residues
1	Gly A:52	-	Pro A:53
2	Cys A:87	-	Pro A:88
3	Gly B:52	-	Pro B:53
4	Cys B:87	-	Pro B:88

(no "SAP(SNP)/Variant" information available for 1XAE)

(no "PROSITE Motif" information available for 1XAE)

(no "Exon" information available for 1XAE)

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:223
 aligned with GFPL2_ZOASP | Q9U6Y4 from UniProtKB/Swiss-Prot  Length:231

    Alignment length:225
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225     
          GFPL2_ZOASP     6 HGLKEEMTMKYHMEGCVNGHKFVITGEGIGYPFKGKQTINLCVIEGGPLPFSEDILSAGFKYGDRIFTEYPQDIVDYFKNSCPAGYTWGRSFLFEDGAVCICNVDITVSVKENCIYHKSIFNGMNFPADGPVMKKMTTNWEASCEKIMPVPKQGILKGDVSMYLLLKDGGRYRCQFDTVYKAKSVPSKMPEWHFIQHKLLREDRSDAKNQKWQLTEHAIAFPSAL 230
               SCOP domains d1xaea_ A: automated matches                                                                                                                                                                                                      SCOP domains
               CATH domains 1xaeA00 A:6-230 Green Fluorescent Protein                                                                                                                                                                                         CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeeeeeeeee..eeeeeeeeeeee....eeeeeeeeee......hhhhhhhhh.--............hhhhhh....eeeeeeeee....eeeeeeeeeee....eeeeeeeeeee............eeee..eeeeeee.....eeeeeeeeeeee....eeeeeeeeeeee..........eeeeeeeeeee.......eeeeeeeeeee.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1xae A   6 HGLKEEMTMKYHMEGcVNGHKFVITGEGIGYPFKGKQTINLcVIEGGPLPFSEDILSAGfk--DRIFTEYPQDIVDYFKNSCPAGYTWGRSFLFEDGAVCICNVDITVSVKENCIYHKSIFNGMNFPADGPVMKKMTTNWEASCEKIMPVPKQGILKGDVSMYLLLKDGGRYRCQFDTVYKAKSVPSKMPEWHFIQHKLLREDRSDAKNQKWQLTEHAIAFPSAL 230
                                    15     |  25        35        45 |      55        65|  |    75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225     
                                          21-CSO                    47-CSO            65-NFA                                                                                                                                                                 
                                                                                       66-CH7

Chain B from PDB  Type:PROTEIN  Length:222
 aligned with GFPL2_ZOASP | Q9U6Y4 from UniProtKB/Swiss-Prot  Length:231

    Alignment length:224
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225    
          GFPL2_ZOASP     6 HGLKEEMTMKYHMEGCVNGHKFVITGEGIGYPFKGKQTINLCVIEGGPLPFSEDILSAGFKYGDRIFTEYPQDIVDYFKNSCPAGYTWGRSFLFEDGAVCICNVDITVSVKENCIYHKSIFNGMNFPADGPVMKKMTTNWEASCEKIMPVPKQGILKGDVSMYLLLKDGGRYRCQFDTVYKAKSVPSKMPEWHFIQHKLLREDRSDAKNQKWQLTEHAIAFPSA 229
               SCOP domains d1xaeb_ B: automated matches                                                                                                                                                                                                     SCOP domains
               CATH domains 1xaeB00 B:6-229 Green Fluorescent Protein                                                                                                                                                                                        CATH domains
           Pfam domains (1) GFP-1xaeB01 B:6-228                                                                                                                                                                                                            - Pfam domains (1)
           Pfam domains (2) GFP-1xaeB02 B:6-228                                                                                                                                                                                                            - Pfam domains (2)
         Sec.struct. author ......eeeeeeeeeee..eeeeeeeeeeee....eeeeeeeeee......hhhhhhhhh.--..............hhhhh...eeeeeeeee....eeeeeeeeeee....eeeeeeeeeee............eeee..eeeeeee.....eeeeeeeeeeee....eeeeeeeeeeee..........eeeeeeeeeee.......eeeeeeeeeee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1xae B   6 HGLKEEMTMKYHMEGcVNGHKFVITGEGIGYPFKGKQTINLcVIEGGPLPFSEDILSAGfk--DRIFTEYPQDIVDYFKNSCPAGYTWGRSFLFEDGAVCICNVDITVSVKENCIYHKSIFNGMNFPADGPVMKKMTTNWEASCEKIMPVPKQGILKGDVSMYLLLKDGGRYRCQFDTVYKAKSVPSKMPEWHFIQHKLLREDRSDAKNQKWQLTEHAIAFPSA 229
                                    15     |  25        35        45 |      55        65|  |    75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225    
                                          21-CSO                    47-CSO            65-NFA                                                                                                                                                                
                                                                                       66-CH7

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(

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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)

Zoanthus sp. [TaxId: 105402] (8)

1a	d1xaea_	A:
1b	d1xaeb_	B:

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Beta (13760)

Architecture: Beta Barrel (4804)

Topology: Green Fluorescent Protein (102)

Homologous Superfamily: Green Fluorescent Protein (102)

Zoanthus sp.. Organism_taxid: 105402. (8)

1a	1xaeA00	A:6-230
1b	1xaeB00	B:6-229

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: GFP (101)

Family: GFP (101)

Zoanthus sp. (Green polyp) (6)

1a	GFP-1xaeB01	B:6-228
1b	GFP-1xaeB02	B:6-228

Asymmetric Unit(hide GO term definitions)

Chain A,B (GFPL2_ZOASP | Q9U6Y4)

biological process
	GO:0008218		bioluminescence		The production of light by certain enzyme-catalyzed reactions in cells.
	GO:0018298		protein-chromophore linkage		The covalent or noncovalent attachment of a chromophore to a protein.

Asymmetric Unit
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	Cis Peptide Bonds
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		Cys B:87 - Pro B:88	[ RasMol ]
		Gly A:52 - Pro A:53	[ RasMol ]
		Gly B:52 - Pro B:53	[ RasMol ]

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	GFPL2_ZOASP \| Q9U6Y4	:	1xa9 2ogr

1xa9	GREEN MUTANT K66M

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