2AHA - JenaLib

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Biological Unit 2 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE ANALYSIS OF A RATE-ENHANCED VARIANT OF REDOX-SENSITIVE GREEN FLUORESCENT PROTEIN IN THE REDUCED FORM, ROGFP1-R8.

Authors :   M. B. Cannon, S. J. Remington

Date :   27 Jul 05 (Deposition) - 21 Mar 06 (Release) - 21 Jan 15 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.98

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

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

Reference :   M. B. Cannon, S. J. Remington
Re-Engineering Redox-Sensitive Green Fluorescent Protein Fo Improved Response Rate.
Protein Sci. V. 15 45 2006
PubMed-ID: 16322566 | Reference-DOI: 10.1110/PS.051734306

Molecule 1 - GREEN FLUORESCENT PROTEIN
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PRSET-B
	Expression System Strain	:	JM109(DE3)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	GFP
	Gene	:	GFP
	Mutation	:	YES
	Organism Scientific	:	AEQUOREA VICTORIA
	Organism Taxid	:	6100

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 6)

No.	Name	Count	Type	Full Name
1	GYS	2	Mod. Amino Acid	[(4Z)-2-(1-AMINO-2-HYDROXYETHYL)-4-(4-HYDROXYBENZYLIDENE)-5-OXO-4,5-DIHYDRO-1H-IMIDAZOL-1-YL]ACETIC ACID
2	SO4	4	Ligand/Ion	SULFATE ION

Biological Unit 1 (2, 2)

No.	Name	Count	Type	Full Name
1	GYS	1	Mod. Amino Acid	[(4Z)-2-(1-AMINO-2-HYDROXYETHYL)-4-(4-HYDROXYBENZYLIDENE)-5-OXO-4,5-DIHYDRO-1H-IMIDAZOL-1-YL]ACETIC ACID
2	SO4	1	Ligand/Ion	SULFATE ION

Biological Unit 2 (2, 4)

No.	Name	Count	Type	Full Name
1	GYS	1	Mod. Amino Acid	[(4Z)-2-(1-AMINO-2-HYDROXYETHYL)-4-(4-HYDROXYBENZYLIDENE)-5-OXO-4,5-DIHYDRO-1H-IMIDAZOL-1-YL]ACETIC ACID
2	SO4	3	Ligand/Ion	SULFATE ION

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	VAL A:55 , PRO A:56 , TRP A:57 , PRO A:58 , HIS A:139 , HOH A:266 , HOH A:304 , HOH A:312	BINDING SITE FOR RESIDUE SO4 A 239
2	AC2	SOFTWARE	PRO B:56 , TRP B:57 , HIS B:139 , HOH B:295	BINDING SITE FOR RESIDUE SO4 B 239
3	AC3	SOFTWARE	LYS B:101 , ASP B:102 , HOH B:253 , HOH B:304	BINDING SITE FOR RESIDUE SO4 B 240
4	AC4	SOFTWARE	GLY A:116 , HIS B:25	BINDING SITE FOR RESIDUE SO4 B 241

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

Asymmetric Unit

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

Asymmetric Unit (4, 8)

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

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

Biological Unit 1 (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)

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

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

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

(no "Exon" information available for 2AHA)

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:226
 aligned with GFP_AEQVI | P42212 from UniProtKB/Swiss-Prot  Length:238

    Alignment length:228
                                    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 SKGEELFTGVVPILVELDGDVNGHKFSVSGEGEGDATYGKLTLKFICTTGKLPVPWPTLVTTFSYGVQCFSRYPDHMKQHDFFKSAMPEGYVQERTIFFKDDGNYKTRAEVKFEGDTLVNRIELKGIDFKEDGNILGHKLEYNYNSHNVYIMADKQKNGIKVNFKIRHNIEDGSVQLADHYQQNTPIGDGPVLLPDNHYLSTQSALSKDPNEKRDHMVLLEFVTAAGI 229
               SCOP domains d2ahaa_ A: Green fluorescent protein, GFP                                                                                                                                                                                            SCOP domains
               CATH domains 2ahaA00 A:2-229 Green Fluorescent Protein                                                                                                                                                                                            CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..hhhhhh.eeeeeeeeeeee..eeeeeeeeeeee....eeeeeeee.......hhhhhh...-.-hhhhh..hhhhhhhhhhhhh....eeeeeeeee....eeeeeeeeeee..eeeeeeeeeee...................eeeeeeee....eeeeeeeeeee.....eeeeeeeeeeee...........eeeeeeeeee........eeeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------Y-------S--------------------------------M-----------------------------------------------------------------------------I---------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2aha A   2 SKGEELFTGVVPILVELDGDVNGHKFSVSGEGEGDATYGDLTLKFISTTGKLPVPWPTLVTTF-s-VQCFSRYPDHMKRHDFFKSAMPEGYVQERTIFFKDDGNYKTRAEVKFEGDTLVNRIELKGIDFKEDGNILGHKLEYNYNCHNVYIMADKQKNGIKVNFKIRHNIEDGSVQLADHYQQNTPIGDGPVLLPDNHYLSTCSALSKDPNEKRDHMVLLERVTAAGI 229
                                    11        21        31        41        51        61  | | | 71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221        
                                                                                         64 | |                                                                                                                                                                 
                                                                                           66-GYS                                                                                                                                                               
                                                                                             68

Chain B from PDB  Type:PROTEIN  Length:226
 aligned with GFP_AEQVI | P42212 from UniProtKB/Swiss-Prot  Length:238

    Alignment length:228
                                    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 SKGEELFTGVVPILVELDGDVNGHKFSVSGEGEGDATYGKLTLKFICTTGKLPVPWPTLVTTFSYGVQCFSRYPDHMKQHDFFKSAMPEGYVQERTIFFKDDGNYKTRAEVKFEGDTLVNRIELKGIDFKEDGNILGHKLEYNYNSHNVYIMADKQKNGIKVNFKIRHNIEDGSVQLADHYQQNTPIGDGPVLLPDNHYLSTQSALSKDPNEKRDHMVLLEFVTAAGI 229
               SCOP domains d2ahab_ B: Green fluorescent protein, GFP                                                                                                                                                                                            SCOP domains
               CATH domains 2ahaB00 B:2-229 Green Fluorescent Protein                                                                                                                                                                                            CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author hhhhhh...eeeeeeeeeeee..eeeeeeeeeeee....eeeeeeee.......hhhhhh...-.-hhhhh..hhhhhhhhhhhhh....eeeeeeeee....eeeeeeeeeee..eeeeeeeeeee..................eeeeeeeee....eeeeeeeeeee.....eeeeeeeeeeee...........eeeeeeeeee........eeeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------Y-------S--------------------------------M-----------------------------------------------------------------------------I---------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2aha B   2 SKGEELFTGVVPILVELDGDVNGHKFSVSGEGEGDATYGDLTLKFISTTGKLPVPWPTLVTTF-s-VQCFSRYPDHMKRHDFFKSAMPEGYVQERTIFFKDDGNYKTRAEVKFEGDTLVNRIELKGIDFKEDGNILGHKLEYNYNCHNVYIMADKQKNGIKVNFKIRHNIEDGSVQLADHYQQNTPIGDGPVLLPDNHYLSTCSALSKDPNEKRDHMVLLERVTAAGI 229
                                    11        21        31        41        51        61  | | | 71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221        
                                                                                         64 | |                                                                                                                                                                 
                                                                                           66-GYS                                                                                                                                                               
                                                                                             68

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
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	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(

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Folds(

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Superfamilies( (-)

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Families(

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Protein Domains( (-)

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Organisms( (-)

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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)

1a	d2ahaa_	A:
1b	d2ahab_	B:

Asymmetric Unit

Classes(

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Architectures( (-)

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Topologies( (-)

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Homologous Superfamilies( (-)

)

Organisms( (-)

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Class: Mainly Beta (13760)

Architecture: Beta Barrel (4804)

Topology: Green Fluorescent Protein (102)

Homologous Superfamily: Green Fluorescent Protein (102)

Aequorea victoria. Organism_taxid: 6100. (30)

1a	2ahaA00	A:2-229
1b	2ahaB00	B:2-229

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

Asymmetric Unit(hide GO term definitions)

Chain A,B (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.

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		Met B:88 - Pro B:89	[ RasMol ]

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	2aha
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1jc0	ROGFP2 IN THE REDUCED FORM.
1jc1	ROGFP2 IN THE OXIDIZED FORM.
2ah8

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 6)

Sites (4, 4)

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (4, 8)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

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SCOP Domains (1, 2)

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Gene Ontology (5, 5)

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