3PIB - JenaLib

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Biological Unit 3 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF RED FLUORESCENT PROTEIN EQFP578 CRYSTALLIZED AT PH 5.5

Authors :   S. Pletnev, N. V. Pletneva, V. Z. Pletnev

Date :   05 Nov 10 (Deposition) - 25 May 11 (Release) - 22 Feb 12 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.15

Chains :   Asym. Unit : A,B,C,D
Biol. Unit 1: A,B,C,D  (1x)
Biol. Unit 2: A,D  (1x)
Biol. Unit 3: B,C  (1x)

Keywords :   Red Fluorescent Protein, Beta-Barrel, Biomarker, Met-Tyr-Gly Chromophore, Sea Anemone, Fluorescent Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   N. V. Pletneva, V. Z. Pletnev, I. I. Shemiakina, D. M. Chudakov, I. Artemyev, A. Wlodawer, Z. Dauter, S. Pletnev
Crystallographic Study Of Red Fluorescent Protein Eqfp578 And Its Far-Red Variant Katushka Reveals Opposite Ph-Induce Isomerization Of Chromophore.
Protein Sci. V. 20 1265 2011
PubMed-ID: 21563226 | Reference-DOI: 10.1002/PRO.654

Molecule 1 - EQFP578 FLUORESCENT PROTEIN
	Chains	:	A, B, C, D
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PQE30
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Organism Common	:	SEA ANEMONES
	Organism Scientific	:	ENTACMAEA QUADRICOLOR
	Organism Taxid	:	6118

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 8)

No.	Name	Count	Type	Full Name
1	GOL	4	Ligand/Ion	GLYCEROL
2	NRQ	4	Mod. Amino Acid	{(4Z)-4-(4-HYDROXYBENZYLIDENE)-2-[3-(METHYLTHIO)PROPANIMIDOYL]-5-OXO-4,5-DIHYDRO-1H-IMIDAZOL-1-YL}ACETIC ACID

Biological Unit 1 (2, 8)

No.	Name	Count	Type	Full Name
1	GOL	4	Ligand/Ion	GLYCEROL
2	NRQ	4	Mod. Amino Acid	{(4Z)-4-(4-HYDROXYBENZYLIDENE)-2-[3-(METHYLTHIO)PROPANIMIDOYL]-5-OXO-4,5-DIHYDRO-1H-IMIDAZOL-1-YL}ACETIC ACID

Biological Unit 2 (2, 4)

No.	Name	Count	Type	Full Name
1	GOL	2	Ligand/Ion	GLYCEROL
2	NRQ	2	Mod. Amino Acid	{(4Z)-4-(4-HYDROXYBENZYLIDENE)-2-[3-(METHYLTHIO)PROPANIMIDOYL]-5-OXO-4,5-DIHYDRO-1H-IMIDAZOL-1-YL}ACETIC ACID

Biological Unit 3 (2, 4)

No.	Name	Count	Type	Full Name
1	GOL	2	Ligand/Ion	GLYCEROL
2	NRQ	2	Mod. Amino Acid	{(4Z)-4-(4-HYDROXYBENZYLIDENE)-2-[3-(METHYLTHIO)PROPANIMIDOYL]-5-OXO-4,5-DIHYDRO-1H-IMIDAZOL-1-YL}ACETIC ACID

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLN A:39 , NRQ A:63 , SER A:66 , LYS A:67 , PHE A:69 , ILE A:70 , HIS A:197 , GLU A:215 , ALA A:217	BINDING SITE FOR RESIDUE GOL A 250
2	AC2	SOFTWARE	GLN B:39 , NRQ B:63 , SER B:66 , LYS B:67 , PHE B:69 , ILE B:70 , HIS B:197 , GLU B:215 , ALA B:217 , HOH B:281	BINDING SITE FOR RESIDUE GOL B 250
3	AC3	SOFTWARE	GLN C:39 , NRQ C:63 , SER C:66 , LYS C:67 , PHE C:69 , ILE C:70 , HIS C:197 , GLU C:215 , ALA C:217	BINDING SITE FOR RESIDUE GOL C 250
4	AC4	SOFTWARE	GLN D:39 , NRQ D:63 , SER D:66 , LYS D:67 , PHE D:69 , ILE D:70 , HIS D:197 , GLU D:215 , ALA D:217	BINDING SITE FOR RESIDUE GOL D 250

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

Asymmetric Unit

No.	Residues
1	Gly A:49	-	Pro A:50
2	Phe A:84	-	Pro A:85
3	Gly B:49	-	Pro B:50
4	Phe B:84	-	Pro B:85
5	Gly C:49	-	Pro C:50
6	Phe C:84	-	Pro C:85
7	Gly D:49	-	Pro D:50
8	Phe D:84	-	Pro D:85

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

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

(no "Exon" information available for 3PIB)

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:227
 aligned with H3JQU4_ENTQU | H3JQU4 from UniProtKB/TrEMBL  Length:223

    Alignment length:229
                                    1                                                                                                                                                                                                                            
                                    |2        12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212         
         H3JQU4_ENTQU     - --------MHMKLYMEGTVNNHHFKCTSEGEGKPYEGTQTMKIKVVEGGPLPFAFDILATSFMYGSKTFINHTQGIPDFFKQSFPEGFTWERITTYEDGGVLTATQDTSLQNGCIIYNVKINGVNFPSNGSVMQKKTLGWEANTEMLYPADGGLRGHSQMALKLVGGGYLHCSFKTTYRSKKPAKNLKMPGFHFVDHRLERIKEADKETYVEQHEMAVAKYCDLPSKLG 221
               SCOP domains d3piba_ A: automated matches                                                                                                                                                                                                          SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eeeeeeeeeee..eeeeeeeeeeee....eeeeeeeeee......hhhhhhhhh.--.....ee.......hhhhh...eeeeeeeee....eeeeeeeeeee..eeeeeeeeeee............eeee..eeeeeeee..eeeeeeeeeeee....eeeeeeeeeeee..hhhhh.....eeeeeeeeeeeee....eeeeeeeeeee......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3pib A   1 SSELIKENMHMKLYMEGTVNNHHFKCTSEGEGKPYEGTQTMKIKVVEGGPLPFAFDILATSFm--SKTFINHTQGIPDFFKQSFPEGFTWERITTYEDGGVLTATQDTSLQNGCIIYNVKINGVNFPSNGSVMQKKTLGWEANTEMLYPADGGLRGHSQMALKLVGGGYLHCSFKTTYRSKKPAKNLKMPGFHFVDHRLERIKEADKETYVEQHEMAVAKYCDLPSKLG 229
                                    10        20        30        40        50        60  |  |  70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220         
                                                                                         63-NRQ

Chain B from PDB  Type:PROTEIN  Length:236
 aligned with H3JQU4_ENTQU | H3JQU4 from UniProtKB/TrEMBL  Length:223

    Alignment length:238
                                           1                                                                                                                                                                                                                              
                                     -     |   5        15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215        
         H3JQU4_ENTQU     - ---------------MHMKLYMEGTVNNHHFKCTSEGEGKPYEGTQTMKIKVVEGGPLPFAFDILATSFMYGSKTFINHTQGIPDFFKQSFPEGFTWERITTYEDGGVLTATQDTSLQNGCIIYNVKINGVNFPSNGSVMQKKTLGWEANTEMLYPADGGLRGHSQMALKLVGGGYLHCSFKTTYRSKKPAKNLKMPGFHFVDHRLERIKEADKETYVEQHEMAVAKYCDLPSKLGHR 223
               SCOP domains d3pibb_ B: automated matches                                                                                                                                                                                                                   SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhh.....eeeeeeeeeee..eeeeeeeeeeee....eeeeeeeeee......hhhhhhhhh.--.....ee.......hhhhh...eeeeeeeee....eeeeeeeeeee..eeeeeeeeeee............eeee..eeeeeeee..eeeeeeeeeeee....eeeeeeeeeeee..hhhhh.....eeeeeeeeeeeee....eeeeeeeeeee........... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3pib B  -6 HHHHHHGSSELIKENMHMKLYMEGTVNNHHFKCTSEGEGKPYEGTQTMKIKVVEGGPLPFAFDILATSFm--SKTFINHTQGIPDFFKQSFPEGFTWERITTYEDGGVLTATQDTSLQNGCIIYNVKINGVNFPSNGSVMQKKTLGWEANTEMLYPADGGLRGHSQMALKLVGGGYLHCSFKTTYRSKKPAKNLKMPGFHFVDHRLERIKEADKETYVEQHEMAVAKYCDLPSKLGHR 231
                                     3        13        23        33        43        53        63  |     73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223        
                                                                                                63-NRQ

Chain C from PDB  Type:PROTEIN  Length:226
 aligned with H3JQU4_ENTQU | H3JQU4 from UniProtKB/TrEMBL  Length:223

    Alignment length:228
                                   1                                                                                                                                                                                                                            
                                   | 3        13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213        
         H3JQU4_ENTQU     - -------MHMKLYMEGTVNNHHFKCTSEGEGKPYEGTQTMKIKVVEGGPLPFAFDILATSFMYGSKTFINHTQGIPDFFKQSFPEGFTWERITTYEDGGVLTATQDTSLQNGCIIYNVKINGVNFPSNGSVMQKKTLGWEANTEMLYPADGGLRGHSQMALKLVGGGYLHCSFKTTYRSKKPAKNLKMPGFHFVDHRLERIKEADKETYVEQHEMAVAKYCDLPSKLG 221
               SCOP domains d3pibc_ C: automated matches                                                                                                                                                                                                         SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .......eeeeeeeeeee..eeeeeeeeeeee....eeeeeeeeee......hhhhhhhhh.--.....ee.......hhhhh...eeeeeeeee....eeeeeeeeeee..eeeeeeeeeee............eeee..eeeeeeee..eeeeeeeeeeee....eeeeeeeeeeee..hhhhh.....eeeeeeeeeeeee....eeeeeeeeeee......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3pib C   2 SELIKENMHMKLYMEGTVNNHHFKCTSEGEGKPYEGTQTMKIKVVEGGPLPFAFDILATSFm--SKTFINHTQGIPDFFKQSFPEGFTWERITTYEDGGVLTATQDTSLQNGCIIYNVKINGVNFPSNGSVMQKKTLGWEANTEMLYPADGGLRGHSQMALKLVGGGYLHCSFKTTYRSKKPAKNLKMPGFHFVDHRLERIKEADKETYVEQHEMAVAKYCDLPSKLG 229
                                    11        21        31        41        51        61 |  |   71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221        
                                                                                        63-NRQ

Chain D from PDB  Type:PROTEIN  Length:228
 aligned with H3JQU4_ENTQU | H3JQU4 from UniProtKB/TrEMBL  Length:223

    Alignment length:230
                                   1                                                                                                                                                                                                                              
                                   | 3        13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223
         H3JQU4_ENTQU     - -------MHMKLYMEGTVNNHHFKCTSEGEGKPYEGTQTMKIKVVEGGPLPFAFDILATSFMYGSKTFINHTQGIPDFFKQSFPEGFTWERITTYEDGGVLTATQDTSLQNGCIIYNVKINGVNFPSNGSVMQKKTLGWEANTEMLYPADGGLRGHSQMALKLVGGGYLHCSFKTTYRSKKPAKNLKMPGFHFVDHRLERIKEADKETYVEQHEMAVAKYCDLPSKLGHR 223
               SCOP domains d3pibd_ D: automated matches                                                                                                                                                                                                           SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeeeeeeeee..eeeeeeeeeeee....eeeeeeeeee......hhhhhhhhh.--.....ee.......hhhhh...eeeeeeeee....eeeeeeeeeee..eeeeeeeeeee............eeee..eeeeeeee..eeeeeeeeeeee....eeeeeeeeeeee..hhhhh.....eeeeeeeeeeeee....eeeeeeeeeee........... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3pib D   2 SELIKENMHMKLYMEGTVNNHHFKCTSEGEGKPYEGTQTMKIKVVEGGPLPFAFDILATSFm--SKTFINHTQGIPDFFKQSFPEGFTWERITTYEDGGVLTATQDTSLQNGCIIYNVKINGVNFPSNGSVMQKKTLGWEANTEMLYPADGGLRGHSQMALKLVGGGYLHCSFKTTYRSKKPAKNLKMPGFHFVDHRLERIKEADKETYVEQHEMAVAKYCDLPSKLGHR 231
                                    11        21        31        41        51        61 |  |   71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231
                                                                                        63-NRQ

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: automated matches (102)

Sea anemone (Entacmaea quadricolor) [TaxId: 6118] (21)

1a	d3piba_	A:
1b	d3pibb_	B:
1c	d3pibc_	C:
1d	d3pibd_	D:

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

(no "Pfam Domain" information available for 3PIB)

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D (H3JQU4_ENTQU | H3JQU4)

biological process
	GO:0008218		bioluminescence		The production of light by certain enzyme-catalyzed reactions in cells.

Asymmetric Unit
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	Ligands, Modified Residues, Ions
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		AC3	[ RasMol ]	+environment [ RasMol ]
		AC4	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
		Gly A:49 - Pro A:50	[ RasMol ]
		Gly B:49 - Pro B:50	[ RasMol ]
		Gly C:49 - Pro C:50	[ RasMol ]
		Gly D:49 - Pro D:50	[ RasMol ]
		Phe A:84 - Pro A:85	[ RasMol ]
		Phe B:84 - Pro B:85	[ RasMol ]
		Phe C:84 - Pro C:85	[ RasMol ]
		Phe D:84 - Pro D:85	[ RasMol ]

Biological Units
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		Biological Unit 2	[ Jena3D ]
		Biological Unit 3	[ Jena3D ]

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3bx9	MONOMERIC FAR-RED FLUORESCENT PROTEIN MKATE CRYSTALLIZED AT PH 2.0
3bxa	MONOMERIC FAR-RED FLUORESCENT PROTEIN MKATE CRYSTALLIZED AT PH 4.2
3bxb	MONOMERIC FAR-RED FLUORESCENT PROTEIN MKATE CRYSTALLIZED AT PH 7.0
3bxc	MONOMERIC FAR-RED FLUORESCENT PROTEIN MKATE CRYSTALLIZED AT PH 9.0
3pj5	FAR-RED FLUORESCENT PROTEIN KATUSHKA CRYSTALLIZED AT PH 5.0
3pj7	FAR-RED FLUORESCENT PROTEIN KATUSHKA CRYSTALLIZED AT PH 8.5
3pjb	FAR-RED FLUORESCENT PROTEIN EQFP578 CRYSTALLIZED AT PH 4.0

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 8)

Sites (4, 4)

SS Bonds (0, 0)

Cis Peptide Bonds (8, 8)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

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SCOP Domains (1, 4)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (1, 1)

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