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Asym./Biol. Unit - manually (Jmol Viewer)

Asym./Biol. Unit (Jmol Viewer)

Asym./Biol. Unit - sites (Jmol Viewer)

Title :   SPECTROSCOPIC AND STRUCTURAL STUDY OF THE HETEROTROPIC LINKAGE BETWEEN HALIDE AND PROTON ION BINDING TO GFP PROTEINS: E2(GFP)-I COMPLEX

Authors :   G. Garau

Date :   29 Nov 06 (Deposition) - 15 May 07 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.94

Chains :   Asym./Biol. Unit : A

Keywords :   Luminescence, Green Fluorescent Protein, Variant, Gfp, E2, Bioluminescence, Photoactive Protein, Fluorescent Chloride, Bromide, Iodine, Halogen, Luminescent Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   D. Arosio, G. Garau, F. Ricci, L. Marchetti, R. Bizzarri, F. Beltram
Spectroscopic And Structural Study Of Proton And Halide Ion Cooperative Binding To Gfp.
Biophys. J. V. 93 232 2007
PubMed-ID: 17434942 | Reference-DOI: 10.1529/BIOPHYSJ.106.102319
(for further references see the PDB file header)

Molecule 1 - GREEN FLUORESCENT PROTEIN
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Gene	:	GFP
	Mutation	:	YES
	Organism Scientific	:	AEQUOREA VICTORIA
	Organism Taxid	:	6100

		1
Asymmetric/Biological Unit	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (2, 10)

No.	Name	Count	Type	Full Name
1	CRO	1	Mod. Amino Acid	{2-[(1R,2R)-1-AMINO-2-HYDROXYPROPYL]-4-(4-HYDROXYBENZYLIDENE)-5-OXO-4,5-DIHYDRO-1H-IMIDAZOL-1-YL}ACETIC ACID
2	IOD	9	Ligand/Ion	IODIDE ION

Asymmetric Unit (7, 7)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	CRO A:1066 , VAL A:1068 , TYR A:1203	BINDING SITE FOR RESIDUE IOD A 1240
2	AC2	SOFTWARE	TYR A:1145 , LEU A:1207	BINDING SITE FOR RESIDUE IOD A 1241
3	AC3	SOFTWARE	ARG A:1215	BINDING SITE FOR RESIDUE IOD A 1244
4	AC4	SOFTWARE	HIS A:1077 , ILE A:1229 , HOH A:1306	BINDING SITE FOR RESIDUE IOD A 1245
5	AC5	SOFTWARE	PHE A:999	BINDING SITE FOR RESIDUE IOD A 1246
6	AC6	SOFTWARE	HOH A:1279	BINDING SITE FOR RESIDUE IOD A 1247
7	AC7	SOFTWARE	ASP A:1180 , PRO A:1192	BINDING SITE FOR RESIDUE IOD A 1248

(no "SS Bond" information available for 2O2B)

Asymmetric/Biological Unit

No.	Residues
1	Met A:1088	-	Pro A:1089

Asymmetric/Biological Unit (4, 4)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_GFP_AEQVI_001 *	F	100	Y	GFP_AEQVI	---	---	A	F	1100	Y
2	UniProt	VAR_GFP_AEQVI_002 *	T	108	S	GFP_AEQVI	---	---	A	T	1108	S
3	UniProt	VAR_GFP_AEQVI_003 *	L	141	M	GFP_AEQVI	---	---	A	L	1141	M
4	UniProt	VAR_GFP_AEQVI_004 *	V	219	I	GFP_AEQVI	---	---	A	V	1219	I
	* ID not provided by source

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(no "PROSITE Motif" information available for 2O2B)

(no "Exon" information available for 2O2B)

Asymmetric/Biological 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:234
 aligned with GFP_AEQVI | P42212 from UniProtKB/Swiss-Prot  Length:238

    Alignment length:236
                                  1                                                                                                                                                                                                                                     
                                  |  4        14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224      
           GFP_AEQVI      - ------MSKGEELFTGVVPILVELDGDVNGHKFSVSGEGEGDATYGKLTLKFICTTGKLPVPWPTLVTTFSYGVQCFSRYPDHMKQHDFFKSAMPEGYVQERTIFFKDDGNYKTRAEVKFEGDTLVNRIELKGIDFKEDGNILGHKLEYNYNSHNVYIMADKQKNGIKVNFKIRHNIEDGSVQLADHYQQNTPIGDGPVLLPDNHYLSTQSALSKDPNEKRDHMVLLEFVTAAGIT  230
               SCOP domains d2o2ba_ A: Green fluorescent protein, GFP                                                                                                                                                                                                    SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------GFP-2o2bA01 A:1005-1229                                                                                                                                                                                                          - Pfam domains
         Sec.struct. author ........hhhhhhh.eeeeeeeeeeee..eeeeeeeeeeee....eeeeeeee.......hhhhhh...--.hhhhh..hhhhhhhhhhhhh....eeeeeeeee....eeeeeeeeeee..eeeeeeeeeee...................eeeeeeeehhhheeeeeeeeeee.....eeeeeeeeeeee...........eeeeeeeeee........eeeeeeeeeee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------Y-------S--------------------------------M-----------------------------------------------------------------------------I----------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                2o2b A  995 GIDPFTVSKGEELFTGVVPILVELDGDVNGHKFSVSGEGEGDATYGKLTLKFICTTGKLPVPWPTLVTTL--gVQCFSRYPDHMKQHDFFKSAMPEGYVQERTIFFKDDGNYKTRAEVKFEGDTLVNRIELKGIDFKEDGNILGHKLEYNYNSHNVYIMADKQKNGIKVNFKIRHNIEDGSVQLADHYQQNTPIGDGPVLLPDNHYLSYQSALSKDPNEKRDHMVLLEFVTAAGIT 1230
                                  1004      1014      1024      1034      1044      1054      1064  ||  1074      1084      1094      1104      1114      1124      1134      1144      1154      1164      1174      1184      1194      1204      1214      1224      
                                                                                              1064  ||                                                                                                                                                                  
                                                                                                 1066-CRO                                                                                                                                                               
                                                                                                  1068

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/Biological 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: Green fluorescent protein, GFP (161)

Jellyfish (Aequorea victoria) [TaxId: 6100] (158)

d2o2ba_

(no "CATH Domain" information available for 2O2B)

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: GFP (101)

Family: GFP (101)

Aequorea victoria (Jellyfish) (53)

GFP-2o2bA01

A:1005-1229

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (GFP_AEQVI | P42212)

molecular function
	GO:0003674	molecular_function	Elemental activities, such as catalysis or binding, describing the actions of a gene product at the molecular level. A given gene product may exhibit one or more molecular functions.
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.
	GO:0018298	protein-chromophore linkage	The covalent or noncovalent attachment of a chromophore to a protein.
cellular component
	GO:0005575	cellular_component	The part of a cell, extracellular environment or virus in which a gene product is located. A gene product may be located in one or more parts of a cell and its location may be as specific as a particular macromolecular complex, that is, a stable, persistent association of macromolecules that function together.

Asymmetric/Biological Unit
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	Cis Peptide Bonds
		Met A:1088 - Pro A:1089	[ RasMol ]

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	2o2b
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Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 10)

Sites (7, 7)

SS Bonds (0, 0)

Cis Peptide Bonds (1, 1)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (4, 4)

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Exons (0, 0)

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