3DPW - JenaLib

Title :   STRUCTURE OF THE YELLOW FLUORESCENT PROTEIN CITRINE FROZEN AT 1 ATMOSPHERE NUMBER 1: STRUCTURE 1 IN A SERIES OF 26 HIGH PRESSURE STRUCTURES

Authors :   B. Barstow, C. U. Kim

Date :   09 Jul 08 (Deposition) - 23 Sep 08 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.59

Chains :   Asym./Biol. Unit : A

Keywords :   Yellow Fluorescent Protein, Beta Barrel, Chromophore, Fluorescent Protein, High Pressure, Luminescence, Photoprotein, Luminescent Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   B. Barstow, N. Ando, C. U. Kim, S. M. Gruner
Alteration Of Citrine Structure By Hydrostatic Pressure Explains The Accompanying Spectral Shift.
Proc. Natl. Acad. Sci. Usa V. 105 13362 2008
PubMed-ID: 18768811 | Reference-DOI: 10.1073/PNAS.0802252105
(for further references see the PDB file header)

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 1)

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

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:231
 aligned with GFP_AEQVI | P42212 from UniProtKB/Swiss-Prot  Length:238

    Alignment length:233
                               1                                                                                                                                                                                                                                     
                               |     7        17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227   
            GFP_AEQVI     - ---MSKGEELFTGVVPILVELDGDVNGHKFSVSGEGEGDATYGKLTLKFICTTGKLPVPWPTLVTTFSYGVQCFSRYPDHMKQHDFFKSAMPEGYVQERTIFFKDDGNYKTRAEVKFEGDTLVNRIELKGIDFKEDGNILGHKLEYNYNSHNVYIMADKQKNGIKVNFKIRHNIEDGSVQLADHYQQNTPIGDGPVLLPDNHYLSTQSALSKDPNEKRDHMVLLEFVTAAGIT 230
               SCOP domains d3dpwa_ A: Green fluorescent protein, GFP                                                                                                                                                                                                 SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhh..eeeeeeeeeee..eeeeeeeeeeeehhh.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
                 3dpw A  -2 DPMVSKGEELFTGVVPILVELDGDVNGHKFSVSGEGEGDATYGKLTLKFICTTGKLPVPWPTLVTTF--gLMCFARYPDHMKQHDFFKSAMPEGYVQERTIFFKDDGNYKTRAEVKFEGDTLVNRIELKGIDFKEDGNILGHKLEYNYNSHNVYIMADKQKNGIKVNFKIRHNIEDGSVQLADHYQQNTPIGDGPVLLPDNHYLSYQSALSKDPNEKRDHMVLLEFVTAAGIT 230
                                     7        17        27        37        47        57      | 66|       77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227   
                                                                                             64  ||                                                                                                                                                                  
                                                                                                66-CR2                                                                                                                                                               
                                                                                                 68

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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 '\|'

Classification and Annotation

SCOP Domains (1, 1)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (5, 5)

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.

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	3dpw
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	GFP_AEQVI \| P42212
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Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File

1f09	CRYSTAL STRUCTURE OF THE GREEN FLUORESCENT PROTEIN (GFP) VARIANT YFP-H148Q WITH TWO BOUND IODIDES
1f0b	CRYSTAL STRUCTURE OF THE GREEN FLUORESCENT PROTEIN (GFP) VARIANT YFP-H148Q
1huy	CRYSTAL STRUCTURE OF CITRINE, AN IMPROVED YELLOW VARIANT OF GREEN FLUORESCENT PROTEIN
1yfp	CRYSTAL STRUCTURE OF YELLOW-EMISSION VARIANT OF GFP, P21212 SPACE GROUP
2yfp	CRYSTAL STRUCTURE OF YELLOW-EMISSION VARIANT OF GFP, P212121 SPACE GROUP
3dpx	STRUCTURE OF THE YELLOW FLUORESCENT PROTEIN CITRINE FROZEN AT 5000 ATMOSPHERES: STRUCTURE 26 IN A SERIES OF 26 HIGH PRESSURE STRUCTURES
3dpz	STRUCTURE OF THE YELLOW FLUORESCENT PROTEIN CITRINE FROZEN AT 4000 ATMOSPHERES NUMBER 3: STRUCTURE 25 IN A SERIES OF 26 HIGH PRESSURE STRUCTURES
3dq1	STRUCTURE OF THE YELLOW FLUORESCENT PROTEIN CITRINE FROZEN AT 4000 ATMOSPHERES NUMBER 2: STRUCTURE 24 IN A SERIES OF 26 HIGH PRESSURE STRUCTURES
3dq2	STRUCTURE OF THE YELLOW FLUORESCENT PROTEIN CITRINE FROZEN AT 4000 ATMOSPHERES NUMBER 1: STRUCTURE 23 IN A SERIES OF 26 HIGH PRESSURE STRUCTURES
3dq3	STRUCTURE OF THE YELLOW FLUORESCENT PROTEIN CITRINE FROZEN AT 2500 ATMOSPHERES: STRUCTURE 22 IN A SERIES OF 26 HIGH PRESSURE STRUCTURES
3dq4	STRUCTURE OF THE YELLOW FLUORESCENT PROTEIN CITRINE FROZEN AT 2000 ATMOSPHERES NUMBER 2: STRUCTURE 20 IN A SERIES OF 26 HIGH PRESSURE STRUCTURES
3dq5	STRUCTURE OF THE YELLOW FLUORESCENT PROTEIN CITRINE FROZEN AT 1960 ATMOSPHERES: STRUCTURE 19 IN A SERIES OF 26 HIGH PRESSURE STRUCTURES
3dq6	STRUCTURE OF THE YELLOW FLUORESCENT PROTEIN CITRINE FROZEN AT 1920 ATMOSPHERES NUMBER 2: STRUCTURE 18 IN A SERIES OF 26 HIGH PRESSURE STRUCTURES
3dq7	STRUCTURE OF THE YELLOW FLUORESCENT PROTEIN CITRINE FROZEN AT 1920 ATMOSPHERES NUMBER 1: STRUCTURE 17 IN A SERIES OF 26 HIGH PRESSURE STRUCTURES
3dq8	STRUCTURE OF THE YELLOW FLUORESCENT PROTEIN CITRINE FROZEN AT 1500 ATMOSPHERES NUMBER 2: STRUCTURE 16 IN A SERIES OF 26 HIGH PRESSURE STRUCTURES
3dq9	STRUCTURE OF THE YELLOW FLUORESCENT PROTEIN CITRINE FROZEN AT 1500 ATMOSPHERES NUMBER 1: STRUCTURE 15 IN A SERIES OF 26 HIGH PRESSURE STRUCTURES
3dqa	STRUCTURE OF THE YELLOW FLUORESCENT PROTEIN CITRINE FROZEN AT 1250 ATMOSPHERES NUMBER 4: STRUCTURE 14 IN A SERIES OF 26 HIGH PRESSURE STRUCTURES
3dqc	STRUCTURE OF THE YELLOW FLUORESCENT PROTEIN CITRINE FROZEN AT 1250 ATMOSPHERES NUMBER 3: STRUCTURE 13 IN A SERIES OF 26 HIGH PRESSURE STRUCTURES
3dqd	STRUCTURE OF THE YELLOW FLUORESCENT PROTEIN CITRINE FROZEN AT 1250 ATMOSPHERES NUMBER 2: STRUCTURE 12 IN A SERIES OF 26 HIGH PRESSURE STRUCTURES
3dqe	STRUCTURE OF THE YELLOW FLUORESCENT PROTEIN CITRINE FROZEN AT 1250 ATMOSPHERES NUMBER 1: STRUCTURE 11 IN A SERIES OF 26 HIGH PRESSURE STRUCTURES
3dqf	STRUCTURE OF THE YELLOW FLUORESCENT PROTEIN CITRINE FROZEN AT 1000 ATMOSPHERES NUMBER 6: STRUCTURE 10 IN A SERIES OF 26 HIGH PRESSURE STRUCTURES
3dqh	STRUCTURE OF THE YELLOW FLUORESCENT PROTEIN CITRINE FROZEN AT 1000 ATMOSPHERES NUMBER 5: STRUCTURE 9 IN A SERIES OF 26 HIGH PRESSURE STRUCTURES
3dqi	STRUCTURE OF THE YELLOW FLUORESCENT PROTEIN CITRINE FROZEN AT 1000 ATMOSPHERES NUMBER 4: STRUCTURE 8 IN A SERIES OF 26 HIGH PRESSURE STRUCTURES
3dqj	STRUCTURE OF THE YELLOW FLUORESCENT PROTEIN CITRINE FROZEN AT 1000 ATMOSPHERES NUMBER 3: STRUCTURE 7 IN A SERIES OF 26 HIGH PRESSURE STRUCTURES
3dqk	STRUCTURE OF THE YELLOW FLUORESCENT PROTEIN CITRINE FROZEN AT 1000 ATMOSPHERES NUMBER 2: STRUCTURE 6 IN A SERIES OF 26 HIGH PRESSURE STRUCTURES
3dql	STRUCTURE OF THE YELLOW FLUORESCENT PROTEIN CITRINE FROZEN AT 1000 ATMOSPHERES NUMBER 1: STRUCTURE 5 IN A SERIES OF 26 HIGH PRESSURE STRUCTURES
3dqm	STRUCTURE OF THE YELLOW FLUORESCENT PROTEIN CITRINE FROZEN AT 750 ATMOSPHERES: STRUCTURE 4 IN A SERIES OF 26 HIGH PRESSURE STRUCTURES
3dqn	STRUCTURE OF THE YELLOW FLUORESCENT PROTEIN CITRINE FROZEN AT 500 ATMOSPHERES: STRUCTURE 3 IN A SERIES OF 26 HIGH PRESSURE STRUCTURES
3dqo	STRUCTURE OF THE YELLOW FLUORESCENT PROTEIN CITRINE FROZEN AT 1 ATMOSPHERE NUMBER 2: STRUCTURE 2 IN A SERIES OF 26 HIGH PRESSURE STRUCTURES
3dqu	STRUCTURE OF THE YELLOW FLUORESCENT PROTEIN CITRINE FROZEN AT 2000 ATMOSPHERES NUMBER 1: STRUCTURE 20 IN A SERIES OF 26 HIGH PRESSURE STRUCTURES

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