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

Asym./Biol. Unit (Jmol Viewer)

Title :   UNCYCLIZED PRECURSOR STRUCTURE OF S65A Y66S R96A GFP VARIANT

Authors :   D. P. Barondeau, C. J. Kassmann, J. A. Tainer, E. D. Getzoff

Date :   08 Jan 05 (Deposition) - 15 Feb 05 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.90

Chains :   Asym./Biol. Unit : A

Keywords :   Chromophore, Uncyclized, Luminescent Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   D. P. Barondeau, C. J. Kassmann, J. A. Tainer, E. D. Getzoff
Understanding Gfp Chromophore Biosynthesis: Controlling Backbone Cyclization And Modifying Post-Translational Chemistry(, ).
Biochemistry V. 44 1960 2005
PubMed-ID: 15697221 | Reference-DOI: 10.1021/BI0479205
(for further references see the PDB file header)

Molecule 1 - GREEN FLUORESCENT PROTEIN
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET11A
	Expression System Strain	:	BL21(DE3)RIL
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Mutation	:	YES
	Organism Scientific	:	AEQUOREA VICTORIA
	Organism Taxid	:	6100
	Other Details	:	S65A, Y66S, R96A, F99S, M153T, V163A

		1
Asymmetric/Biological Unit	:	A

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 1YHI)

(no "Site" information available for 1YHI)

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

Asymmetric/Biological Unit

No.	Residues
1	Met A:88	-	Pro A:89

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	100	Y
2	UniProt	VAR_GFP_AEQVI_002 *	T	108	S	GFP_AEQVI	---	---	A	T	108	S
3	UniProt	VAR_GFP_AEQVI_003 *	L	141	M	GFP_AEQVI	---	---	A	L	141	M
4	UniProt	VAR_GFP_AEQVI_004 *	V	219	I	GFP_AEQVI	---	---	A	V	219	I
	* ID not provided by source

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

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

(no "Exon" information available for 1YHI)

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:227
 aligned with GFP_AEQVI | P42212 from UniProtKB/Swiss-Prot  Length:238

    Alignment length:227
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       
            GFP_AEQVI     2 SKGEELFTGVVPILVELDGDVNGHKFSVSGEGEGDATYGKLTLKFICTTGKLPVPWPTLVTTFSYGVQCFSRYPDHMKQHDFFKSAMPEGYVQERTIFFKDDGNYKTRAEVKFEGDTLVNRIELKGIDFKEDGNILGHKLEYNYNSHNVYIMADKQKNGIKVNFKIRHNIEDGSVQLADHYQQNTPIGDGPVLLPDNHYLSTQSALSKDPNEKRDHMVLLEFVTAAG 228
               SCOP domains d1yhia_ A: automated matches                                                                                                                                                                                                        SCOP domains
               CATH domains 1yhiA00 A:2-228 Green Fluorescent Protein                                                                                                                                                                                           CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhh..eeeeeeeeeee..eeeeeeeeeeee....eeeeeeee.......hhhhhhhhhhhhhhhhh..hhhhhhhhhhhhh....eeeeeeeee....eeeeeeeeeee..eeeeeeeeeee...................eeeeeeeehhhheeeeeeeeeee.....eeeeeeeeeeee...........eeeeeeeeee........eeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------Y-------S--------------------------------M-----------------------------------------------------------------------------I--------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1yhi A   2 SKGEELFTGVVPILVELDGDVNGHKFSVSGEGEGDATYGKLTLKFICTTGKLPVPWPTLVTTFASGVQCFSRYPDHMKQHDFFKSAMPEGYVQEATISFKDDGNYKTRAEVKFEGDTLVNRIELKGIDFKEDGNILGHKLEYNYNSHNVYITADKQKNGIKANFKIRHNIEDGSVQLADHYQQNTPIGDGPVLLPDNHYLSTQSALSKDPNEKRDHMVLLEFVTAAG 228
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221

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: automated matches (102)

Jellyfish (Aequorea victoria) [TaxId: 6100] (34)

d1yhia_

Asymmetric/Biological 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)

Aequorea victoria. Organism_taxid: 6100. (34)

1yhiA00

A:2-228

(no "Pfam Domain" information available for 1YHI)

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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	Ligands, Modified Residues, Ions
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	Sites
(no "Sites" information available for 1yhi)

	Cis Peptide Bonds
		Met A:88 - Pro A:89	[ RasMol ]

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	1yhi
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	GFP_AEQVI \| P42212
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1yhg	UNCYCLIZED PRECURSOR STRUCTURE OF S65G Y66S V68G VARIANT
1yhh	UNCYCLIZED PRECURSOR STRUCTURE OF S65A Y66S G67A VARIANT
1yj2
1yjf

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (0, 0)

Sites (0, 0)

SS Bonds (0, 0)

Cis Peptide Bonds (1, 1)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (4, 4)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (1, 1)

CATH Domains (1, 1)

Pfam Domains (0, 0)

Gene Ontology (5, 5)

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