2DD9 - JenaLib

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Title :   A MUTANT OF GFP-LIKE PROTEIN FROM CHIRIDIUS POPPEI

Authors :   K. Suto, H. Masuda, Y. Takenaka, H. Mizuno

Date :   24 Jan 06 (Deposition) - 23 Jan 07 (Release) - 30 Jun 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.30

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

Keywords :   Gfp-Like Protein, Fluorescent Protein, Luminescent Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   K. Suto, H. Masuda, Y. Takenaka, F. I. Tsuji, H. Mizuno
Structural Basis For Red-Shifted Emission Of A Gfp-Like Protein From The Marine Copepod Chiridius Poppei
Genes Cells V. 14 727 2009
PubMed-ID: 19469881 | Reference-DOI: 10.1111/J.1365-2443.2009.01305.X
(for further references see the PDB file header)

Molecule 1 - GREEN FLUORESCENT PROTEIN
	Chains	:	A, B, C, D
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET-101
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Mutation	:	YES
	Organism Scientific	:	CHIRIDIUS POPPEI
	Organism Taxid	:	286301
	Synonym	:	YELLOWISH-GREEN FLUORESCENT PROTEIN

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 10)

No.	Name	Count	Type	Full Name
1	CL	1	Ligand/Ion	CHLORIDE ION
2	CR2	4	Mod. Amino Acid	{(4Z)-2-(AMINOMETHYL)-4-[(4-HYDROXYPHENYL)METHYLIDENE]-5-OXO-4,5-DIHYDRO-1H-IMIDAZOL-1-YL}ACETIC ACID
3	CXS	5	Ligand/Ion	3-CYCLOHEXYL-1-PROPYLSULFONIC ACID

Biological Unit 1 (2, 6)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION
2	CR2	2	Mod. Amino Acid	{(4Z)-2-(AMINOMETHYL)-4-[(4-HYDROXYPHENYL)METHYLIDENE]-5-OXO-4,5-DIHYDRO-1H-IMIDAZOL-1-YL}ACETIC ACID
3	CXS	4	Ligand/Ion	3-CYCLOHEXYL-1-PROPYLSULFONIC ACID

Biological Unit 2 (2, 3)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION
2	CR2	2	Mod. Amino Acid	{(4Z)-2-(AMINOMETHYL)-4-[(4-HYDROXYPHENYL)METHYLIDENE]-5-OXO-4,5-DIHYDRO-1H-IMIDAZOL-1-YL}ACETIC ACID
3	CXS	1	Ligand/Ion	3-CYCLOHEXYL-1-PROPYLSULFONIC ACID

Asymmetric Unit (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	LYS A:18 , LYS B:18	BINDING SITE FOR RESIDUE CL B 1006
2	AC2	SOFTWARE	LEU A:141 , ALA A:149 , LYS A:169 , ALA B:153 , THR B:165 , GLU B:167 , HOH B:1209 , HOH B:1401 , HOH B:1458 , GLN C:122	BINDING SITE FOR RESIDUE CXS B 1001
3	AC3	SOFTWARE	SER A:144 , PRO B:124 , LYS B:127 , THR B:129 , LEU B:158 , ASP B:160 , SER B:162 , HOH B:1169 , GLU C:90	BINDING SITE FOR RESIDUE CXS B 1002
4	AC4	SOFTWARE	THR A:84 , ASN A:98 , ARG A:100 , ASN A:171 , ASP A:173 , LYS C:127 , ASP C:128	BINDING SITE FOR RESIDUE CXS A 1003
5	AC5	SOFTWARE	THR B:82 , THR B:84 , ASN B:98 , ARG B:100 , ASP B:173 , LYS D:127	BINDING SITE FOR RESIDUE CXS B 1004
6	AC6	SOFTWARE	PRO A:124 , LYS A:127 , THR A:129 , LEU A:158 , ASP A:160 , SER A:162 , HOH A:1085 , SER B:144 , GLU D:90 , PRO D:124	BINDING SITE FOR RESIDUE CXS D 1005

(no "SS Bond" information available for 2DD9)

(no "Cis Peptide Bond" information available for 2DD9)

(no "SAP(SNP)/Variant" information available for 2DD9)

(no "PROSITE Motif" information available for 2DD9)

(no "Exon" information available for 2DD9)

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:215
 aligned with Q2MHN7_9MAXI | Q2MHN7 from UniProtKB/TrEMBL  Length:219

    Alignment length:217
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       
         Q2MHN7_9MAXI     2 TTFKIESRIHGNLNGEKFELVGGGVGEEGRLEIEMKTKDKPLAFSPFLLSHCMGYGFYHFASFPKGTKNIYLHAATNGGYTNTRKEIYEDGGILEVNFRYTYEFNKIIGDVECIGHGFPSQSPIFKDTIVKSCPTVDLMLPMSGNIIASSYARAFQLKDGSFYTAEVKNNIDFKNPIHESFSKSGPMFTHRRVEETHTKENLAMVEYQQVFNSAPRD 218
               SCOP domains d2dd9a_ A: automated matches                                                                                                                                                                                              SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeeeee..eeeeeeeeeeee..eeeeeeee.......hhhhhhhhh--.hhh.ee......hhhhhhhh...eeeeeeeee....eeeeeeeeeee..eeeeeeeeeee.....hhhhhh.eeee..eeeeeeee...eeeeeeeeeeee....eeeeeeeeeeee.............eeeeeeeeeee...eeeeeeeeeee...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2dd9 A   2 TTFKIESRIHGNLNGEKFELVGGGVGEEGRLEIEMKTKDKPLAFSPFLLSTCM--gFYHFASFPKGTKNIYLHAATNGGYTNTRKEIYEDGGILEVNFRYTYEFNKIIGDVECIGHGFPSQSPIFKDTIVKSCPTVDLMLPMSGNIIASSYARAFQLKDGSFYTAEVKNNIDFKNPIHESFSKSGPMFTHRRVEETHTKENLAMVEYQQVFNSAPRD 218
                                    11        21        31        41        51  |  || 61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       
                                                                               54  ||                                                                                                                                                                
                                                                                  56-CR2                                                                                                                                                             
                                                                                   58

Chain B from PDB  Type:PROTEIN  Length:215
 aligned with Q2MHN7_9MAXI | Q2MHN7 from UniProtKB/TrEMBL  Length:219

    Alignment length:217
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       
         Q2MHN7_9MAXI     2 TTFKIESRIHGNLNGEKFELVGGGVGEEGRLEIEMKTKDKPLAFSPFLLSHCMGYGFYHFASFPKGTKNIYLHAATNGGYTNTRKEIYEDGGILEVNFRYTYEFNKIIGDVECIGHGFPSQSPIFKDTIVKSCPTVDLMLPMSGNIIASSYARAFQLKDGSFYTAEVKNNIDFKNPIHESFSKSGPMFTHRRVEETHTKENLAMVEYQQVFNSAPRD 218
               SCOP domains d2dd9b_ B: automated matches                                                                                                                                                                                              SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeeeee..eeeeeeeeeeee..eeeeeeee.......hhhhhh...--.hhh.ee......hhhhhhhhh..eeeeeeeee....eeeeeeeeeee..eeeeeeeeeee.....hhhhhh.eeee..eeeeeeee...eeeeeeeeeeee....eeeeeeeeeeee.............eeeeeeeeeee...eeeeeeeeeee...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2dd9 B   2 TTFKIESRIHGNLNGEKFELVGGGVGEEGRLEIEMKTKDKPLAFSPFLLSTCM--gFYHFASFPKGTKNIYLHAATNGGYTNTRKEIYEDGGILEVNFRYTYEFNKIIGDVECIGHGFPSQSPIFKDTIVKSCPTVDLMLPMSGNIIASSYARAFQLKDGSFYTAEVKNNIDFKNPIHESFSKSGPMFTHRRVEETHTKENLAMVEYQQVFNSAPRD 218
                                    11        21        31        41        51  |  || 61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       
                                                                               54  ||                                                                                                                                                                
                                                                                  56-CR2                                                                                                                                                             
                                                                                   58

Chain C from PDB  Type:PROTEIN  Length:214
 aligned with Q2MHN7_9MAXI | Q2MHN7 from UniProtKB/TrEMBL  Length:219

    Alignment length:216
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211      
         Q2MHN7_9MAXI     2 TTFKIESRIHGNLNGEKFELVGGGVGEEGRLEIEMKTKDKPLAFSPFLLSHCMGYGFYHFASFPKGTKNIYLHAATNGGYTNTRKEIYEDGGILEVNFRYTYEFNKIIGDVECIGHGFPSQSPIFKDTIVKSCPTVDLMLPMSGNIIASSYARAFQLKDGSFYTAEVKNNIDFKNPIHESFSKSGPMFTHRRVEETHTKENLAMVEYQQVFNSAPR 217
               SCOP domains d2dd9c_ C: automated matches                                                                                                                                                                                             SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeeeeeeeee..eeeeeeeeeeee..eeeeeeee.......hhhhhh...--.hhh.ee......hhhhhhhhh..eeeeeeeee....eeeeeeeeeee..eeeeeeeeeee.....hhhhh..eeee..eeeeeee....eeeeeeeeeeee....eeeeeeeeeeee.............eeeeeeeeeee...eeeeeeeeeee..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2dd9 C   2 TTFKIESRIHGNLNGEKFELVGGGVGEEGRLEIEMKTKDKPLAFSPFLLSTCM--gFYHFASFPKGTKNIYLHAATNGGYTNTRKEIYEDGGILEVNFRYTYEFNKIIGDVECIGHGFPSQSPIFKDTIVKSCPTVDLMLPMSGNIIASSYARAFQLKDGSFYTAEVKNNIDFKNPIHESFSKSGPMFTHRRVEETHTKENLAMVEYQQVFNSAPR 217
                                    11        21        31        41        51  |  || 61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211      
                                                                               54  ||                                                                                                                                                               
                                                                                  56-CR2                                                                                                                                                            
                                                                                   58

Chain D from PDB  Type:PROTEIN  Length:215
 aligned with Q2MHN7_9MAXI | Q2MHN7 from UniProtKB/TrEMBL  Length:219

    Alignment length:217
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       
         Q2MHN7_9MAXI     2 TTFKIESRIHGNLNGEKFELVGGGVGEEGRLEIEMKTKDKPLAFSPFLLSHCMGYGFYHFASFPKGTKNIYLHAATNGGYTNTRKEIYEDGGILEVNFRYTYEFNKIIGDVECIGHGFPSQSPIFKDTIVKSCPTVDLMLPMSGNIIASSYARAFQLKDGSFYTAEVKNNIDFKNPIHESFSKSGPMFTHRRVEETHTKENLAMVEYQQVFNSAPRD 218
               SCOP domains d2dd9d_ D: automated matches                                                                                                                                                                                              SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeeeeee..eeeeeeeeeeee..eeeeeeee.......hhhhhhhhh--.hhh.ee......hhhhhhhh...eeeeeeeee....eeeeeeeeeee..eeeeeeeeeee.....hhhhh..eeee..eeeeeee....eeeeeeeeeeee....eeeeeeeeeeee.............eeeeeeeeeee...eeeeeeeeeee...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2dd9 D   2 TTFKIESRIHGNLNGEKFELVGGGVGEEGRLEIEMKTKDKPLAFSPFLLSTCM--gFYHFASFPKGTKNIYLHAATNGGYTNTRKEIYEDGGILEVNFRYTYEFNKIIGDVECIGHGFPSQSPIFKDTIVKSCPTVDLMLPMSGNIIASSYARAFQLKDGSFYTAEVKNNIDFKNPIHESFSKSGPMFTHRRVEETHTKENLAMVEYQQVFNSAPRD 218
                                    11        21        31        41        51  |  || 61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       
                                                                               54  ||                                                                                                                                                                
                                                                                  56-CR2                                                                                                                                                             
                                                                                   58

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)

Chiridius poppei [TaxId: 286301] (2)

1a	d2dd9a_	A:
1b	d2dd9b_	B:
1c	d2dd9c_	C:
1d	d2dd9d_	D:

(no "CATH Domain" information available for 2DD9)

(no "Pfam Domain" information available for 2DD9)

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D (Q2MHN7_9MAXI | Q2MHN7)

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

Asymmetric Unit
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	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2dd9)

Biological Units
	Complete Structure
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	Q2MHN7_9MAXI \| Q2MHN7	:	2dd7

2dd7	WILD-TYPE OF THIS PROTEIN.

Description

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Chains, Units

Ligands, Modified Residues, Ions (3, 10)

Sites (6, 6)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

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