3VK1 - JenaLib

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Title :   GREEN-FLUORESCENT VARIANT OF THE NON-FLUORESCENT CHROMOPROTEIN RTMS5

Authors :   J. M. Battad, D. A. K. Traore, M. Wilce, M. Byres, J. Rossjohn, R. J. Deven M. Prescott

Date :   07 Nov 11 (Deposition) - 06 Jun 12 (Release) - 02 Nov 16 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.20

Chains :   Asym. Unit : A
Biol. Unit 1: A  (4x)

Keywords :   Gfp, Anthozoa, Beta Can, Beta Barrel, Fluorescent Protein, Pigment Protein, Pigment, Pocilloporin, Chromoprotein, Luminescent Protein, Fluorophore, Chromophore, Acylimine (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. M. Battad, D. A. Traore, E. Byres, J. Rossjohn, R. J. Devenish, S. Olsen, M. C. Wilce, M. Prescott
A Green Fluorescent Protein Containing A Qfg Tri-Peptide Chromophore: Optical Properties And X-Ray Crystal Structure
Plos One V. 7 47331 2012
PubMed-ID: 23071789 | Reference-DOI: 10.1371/JOURNAL.PONE.0047331

Molecule 1 - GFP-LIKE NON-FLUORESCENT CHROMOPROTEIN
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PQE10BN
	Expression System Strain	:	NOVA BLUE
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	RTMS5
	Mutation	:	YES
	Organism Common	:	CORAL
	Organism Scientific	:	MONTIPORA EFFLORESCENS
	Organism Taxid	:	105610
	Synonym	:	NON-FLUORESCENT POCILLOPORIN, RTMS 5

		1
Asymmetric Unit	:	A
Biological Unit 1 (4x)	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 5)

No.	Name	Count	Type	Full Name
1	CL	3	Ligand/Ion	CHLORIDE ION
2	IOD	1	Ligand/Ion	IODIDE ION
3	QFG	1	Mod. Amino Acid	{(4E)-2-[(1E)-4-AMINO-4-OXOBUTANIMIDOYL]-4-BENZYLIDENE-5-OXO-4,5-DIHYDRO-1H-IMIDAZOL-1-YL}ACETIC ACID

Biological Unit 1 (2, 8)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION
2	IOD	4	Ligand/Ion	IODIDE ION
3	QFG	4	Mod. Amino Acid	{(4E)-2-[(1E)-4-AMINO-4-OXOBUTANIMIDOYL]-4-BENZYLIDENE-5-OXO-4,5-DIHYDRO-1H-IMIDAZOL-1-YL}ACETIC ACID

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASN A:205	BINDING SITE FOR RESIDUE IOD A 226
2	AC2	SOFTWARE	SER A:146	BINDING SITE FOR RESIDUE CL A 227
3	AC3	SOFTWARE	LYS A:182	BINDING SITE FOR RESIDUE CL A 228
4	AC4	SOFTWARE	GLY A:155	BINDING SITE FOR RESIDUE CL A 229

(no "SS Bond" information available for 3VK1)

Asymmetric Unit

No.	Residues
1	Gly A:52	-	Pro A:53
2	Phe A:87	-	Pro A:88

(no "SAP(SNP)/Variant" information available for 3VK1)

(no "PROSITE Motif" information available for 3VK1)

(no "Exon" information available for 3VK1)

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:217
 aligned with NFCP_MONEF | P83690 from UniProtKB/Swiss-Prot  Length:221

    Alignment length:219
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212         
           NFCP_MONEF     3 VIATQMTYKVYMSGTVNGHYFEVEGDGKGRPYEGEQTVKLTVTKGGPLPFAWDILSPQCQYGSIPFTKYPEDIPDYVKQSFPEGFTWERIMNFEDGAVCTVSNDSSIQGNCFTYHVKFSGLNFPPNGPVMQKKTQGWEPHSERLFARGGMLIGNNFMALKLEGGGHYLCEFKTTYKAKKPVKMPGYHYVDRKLDVTNHNKDYTSVEQCEISIARKPVVA 221
               SCOP domains d3vk1a_ A: automated matches                                                                                                                                                                                                SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeeeeeeeee..eeeeeeeeeee.....eeeeeeeeee......hhhhhhhhh.--............hhhhhh....eeeeeeeee....eeeeeeeeeee..eeeeeeeeeee............eeee..eeeeeeee..eeeeeeeeeeee....eeeeeeeeeeee.........eeeeeeeeeeee.....eeeeeeeeeee..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3vk1 A   7 VIATQMTYKVYMSGTVNGHYFEVEGDGKGRPYEGEQTVKLTVTKGGPLPFAWDILSPQCq--SIPFTKYPEDIPDYVKQSFPEGFTWERIMNFEDGAVCTVSNDSSIQGNCFTYHVKFSGLNFPPNGPVMQKKTQGWEPSSERLFARGGMLIGNNFMALKLEGGGHYLCEFKTTYKAKKPVKMPGYHYVDRKLDVTNHNKDYTSVEQCEISIARKPVVA 225
                                    16        26        36        46        56        66  |     76        86        96       106       116       126       136       146       156       166       176       186       196       206       216         
                                                                                      66-QFG

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)

Coral (Montipora efflorescens) [TaxId: 105610] (3)

d3vk1a_

(no "CATH Domain" information available for 3VK1)

(no "Pfam Domain" information available for 3VK1)

Asymmetric Unit(hide GO term definitions)

Chain A (NFCP_MONEF | P83690)

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:0010117	photoprotection	Protection mechanism used by plants under conditions of excess energy absorption as a consequence of the light reactions of photosynthesis.
	GO:0018298	protein-chromophore linkage	The covalent or noncovalent attachment of a chromophore to a protein.
cellular component
	GO:0018995	host	Any organism in which another organism, especially a parasite or symbiont, spends part or all of its life cycle and from which it obtains nourishment and/or protection.

Asymmetric Unit
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	Ligands, Modified Residues, Ions
		CL	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		IOD	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		QFG	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]
		AC2	[ RasMol ]	+environment [ RasMol ]
		AC3	[ RasMol ]	+environment [ RasMol ]
		AC4	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
		Gly A:52 - Pro A:53	[ RasMol ]
		Phe A:87 - Pro A:88	[ RasMol ]

Biological Unit
	Complete Structure
		Biological Unit 1	[ Jena3D ]

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	3vk1
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		Domain Information	:	XDom
		Interatomic Contacts of Structural Units	:	CSU
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	NFCP_MONEF \| P83690
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UniProtKB/Swiss-Prot
	NFCP_MONEF \| P83690	:	1mou 1mov 2arl 2p4m 3vic

1mou	CRYSTAL STRUCTURE OF WILD-TYPE RTMS5
1mov	CRYSTAL STRUCTURE OF RTMS5 H146S
2arl	CRYSTAL STRUCTURE OF RTMS5 H146S AT PH 3.5
2p4m	CRYSTAL STRUCTURE OF RTMS5 H146S AT HIGH PH
3vic	GREEN-FLUORESCENT VARIANT OF RTMS5

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 5)

Sites (4, 4)

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

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SCOP Domains (1, 1)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (5, 5)

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Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File