4LJB - JenaLib

Asym./Biol. Unit (Jmol Viewer)

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

Title :   STRUCTURE OF A PHOTOBLEACHED STATE OF IRISFP UNDER HIGH INTENSITY LASER-LIGHT

Authors :   C. Duan, V. Adam, M. Byrdin, J. Ridard, S. Kieffer-Jacquinod, C. Morlot D. Arcizet, I. Demachy, D. Bourgeois

Date :   04 Jul 13 (Deposition) - 09 Oct 13 (Release) - 06 Nov 13 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.90

Chains :   Asym./Biol. Unit : A,B,C,D

Keywords :   Fluorescent Protein, Photobleaching, Beta-Barrel, Decarboxylation (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   C. Duan, V. Adam, M. Byrdin, J. Ridard, S. Kieffer-Jaquinod, C. Morlot D. Arcizet, I. Demachy, D. Bourgeois
Structural Evidence For A Two-Regime Photobleaching Mechanism In A Reversibly Switchable Fluorescent Protein.
J. Am. Chem. Soc. V. 135 15841 2013
PubMed-ID: 24059326 | Reference-DOI: 10.1021/JA406860E

Molecule 1 - GREEN TO RED PHOTOCONVERTIBLE GPF-LIKE PROTEIN EOSFP
	Chains	:	A, B, C, D
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Organism Common	:	LOBED BRAIN CORAL
	Organism Scientific	:	LOBOPHYLLIA HEMPRICHII
	Organism Taxid	:	46758

		1	2	3	4
Asymmetric/Biological Unit	:	A	B	C	D

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (3, 20)

No.	Name	Count	Type	Full Name
1	CR8	4	Mod. Amino Acid	2-[1-AMINO-2-(1H-IMIDAZOL-5-YL)ETHYL]-1-(CARBOXYMETHYL)-4-[(4-OXOCYCLOHEXA-2,5-DIEN-1-YLIDENE)METHYL]-1H-IMIDAZOL-5-OLATE
2	SO3	3	Ligand/Ion	SULFITE ION
3	SO4	13	Ligand/Ion	SULFATE ION

Asymmetric Unit (15, 15)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	ASN A:17 , HIS A:22 , HOH A:468 , HOH A:480 , ARG C:104	BINDING SITE FOR RESIDUE SO4 A 301
02	AC2	SOFTWARE	LYS A:182 , GLY A:183 , HOH A:465	BINDING SITE FOR RESIDUE SO4 A 303
03	AC3	SOFTWARE	CYS A:195 , ILE A:196 , GLU A:197 , TYR A:211	BINDING SITE FOR RESIDUE SO3 A 304
04	AC4	SOFTWARE	ARG A:149 , ASP A:150 , ALA B:167	BINDING SITE FOR RESIDUE SO4 A 305
05	AC5	SOFTWARE	ALA A:167 , ARG B:149 , ASP B:150	BINDING SITE FOR RESIDUE SO4 B 301
06	AC6	SOFTWARE	GLY B:16 , ASN B:17 , HIS B:22 , ARG D:104	BINDING SITE FOR RESIDUE SO4 B 302
07	AC7	SOFTWARE	LYS B:182 , GLY B:183	BINDING SITE FOR RESIDUE SO4 B 303
08	AC8	SOFTWARE	HOH B:464	BINDING SITE FOR RESIDUE SO3 B 304
09	AC9	SOFTWARE	GLY C:16 , ASN C:17 , HIS C:22	BINDING SITE FOR RESIDUE SO4 C 301
10	BC1	SOFTWARE	ASP C:202 , LYS C:203 , HOH C:440	BINDING SITE FOR RESIDUE SO4 C 302
11	BC2	SOFTWARE	GLU A:70 , HOH A:437 , TYR C:78 , VAL C:184 , LEU C:186 , HOH C:417	BINDING SITE FOR RESIDUE SO4 C 303
12	BC3	SOFTWARE	GLU C:197 , TYR C:211 , PRO D:221	BINDING SITE FOR RESIDUE SO3 C 304
13	BC4	SOFTWARE	ALA C:167 , ASP D:150	BINDING SITE FOR RESIDUE SO4 C 305
14	BC5	SOFTWARE	ASN D:17 , HIS D:121	BINDING SITE FOR RESIDUE SO4 D 301
15	BC6	SOFTWARE	ASP D:202 , LYS D:203 , HOH D:452	BINDING SITE FOR RESIDUE SO4 D 302

(no "SS Bond" information available for 4LJB)

Asymmetric/Biological Unit

No.	Residues
1	Gly A:48	-	Pro A:49
2	Phe A:83	-	Pro A:84
3	Leu A:220	-	Pro A:221
4	Gly B:48	-	Pro B:49
5	Phe B:83	-	Pro B:84
6	Leu B:220	-	Pro B:221
7	Gly C:48	-	Pro C:49
8	Phe C:83	-	Pro C:84
9	Leu C:220	-	Pro C:221
10	Gly D:48	-	Pro D:49
11	Phe D:83	-	Pro D:84
12	Leu D:220	-	Pro D:221

(no "SAP(SNP)/Variant" information available for 4LJB)

(no "PROSITE Motif" information available for 4LJB)

(no "Exon" information available for 4LJB)

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:221
                                                                                                                                                                                                                                                             
               SCOP domains d4ljba_ A: automated matches                                                                                                                                                                                                  SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeeeeeeeee..eeeeeeeeeeeehhh.eeeeeeeeee......hhhhhh..................hhhhh...eeeeeeeee....eeeeeeeeeee..eeeeeeeeeee............eeee..eeeeeeee..eeeeeeeeeeee...eeeeeeeeeeeee..........eeeeeeeeeeee.....eeeeeeeeeee...... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ljb A   1 MSAIKPDMKINLRMEGNVNGHHFVIDGDGTGKPFEGKQSMDLEVKEGGPLPFAFDILTTAFhNRVFAEYPDHIQDYFKQSFPKGYSWERSLTFEDGGICIARNDITMEGDTFYNKVRFHGVNFPANGPVMQKKTLKWEPSTEKMYVRDGVLTGDITMALLLEGNAHYRCDSRTTYKAKEKGVKLPGYHLVDHCIEILSHDKDYNKVKLYEHAVAHSGLPDN 223
                                    10        20        30        40        50        60||      72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222 
                                                                                       61|                                                                                                                                                               
                                                                                        64-CR8

Chain B from PDB  Type:PROTEIN  Length:220
                                                                                                                                                                                                                                                            
               SCOP domains d4ljbb_ B: automated matches                                                                                                                                                                                                 SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeeeeeeeee..eeeeeeeeeeeehhh.eeeeeeeeee......hhhhhhhhh.......................eeeeeeeee....eeeeeeeeeee..eeeeeeeeeee.....hhhhhh.eeee..eeeeeeee..eeeeeeeeeeee...eeeeeeeeeeeee..........eeeeeeeeeeee.....eeeeeeeeeee...... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ljb B   2 SAIKPDMKINLRMEGNVNGHHFVIDGDGTGKPFEGKQSMDLEVKEGGPLPFAFDILTTAFhNRVFAEYPDHIQDYFKQSFPKGYSWERSLTFEDGGICIARNDITMEGDTFYNKVRFHGVNFPANGPVMQKKTLKWEPSTEKMYVRDGVLTGDITMALLLEGNAHYRCDSRTTYKAKEKGVKLPGYHLVDHCIEILSHDKDYNKVKLYEHAVAHSGLPDN 223
                                    11        21        31        41        51        61|       73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223
                                                                                      61|                                                                                                                                                               
                                                                                       64-CR8

Chain C from PDB  Type:PROTEIN  Length:223
                                                                                                                                                                                                                                                               
               SCOP domains d4ljbc_ C: automated matches                                                                                                                                                                                                    SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........eeeeeeeeeee..eeeeeeeeeeee....eeeeeeeeee......hhhhh.................hhhhhh....eeeeeeeee....eeeeeeeeeee..eeeeeeeeeee............eeee..eeeeeeee..eeeeeeeeeeee....eeeeeeeeeeee..........eeeeeeeeeeee.....eeeeeeeeeee...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ljb C  -1 HHMSAIKPDMKINLRMEGNVNGHHFVIDGDGTGKPFEGKQSMDLEVKEGGPLPFAFDILTTAFhNRVFAEYPDHIQDYFKQSFPKGYSWERSLTFEDGGICIARNDITMEGDTFYNKVRFHGVNFPANGPVMQKKTLKWEPSTEKMYVRDGVLTGDITMALLLEGNAHYRCDSRTTYKAKEKGVKLPGYHLVDHCIEILSHDKDYNKVKLYEHAVAHSGLPDN 223
                                     8        18        28        38        48        58  ||    70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220   
                                                                                         61|                                                                                                                                                               
                                                                                          64-CR8

Chain D from PDB  Type:PROTEIN  Length:221
                                                                                                                                                                                                                                                             
               SCOP domains d4ljbd_ D: automated matches                                                                                                                                                                                                  SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeeeeeeeee..eeeeeeeeeeee....eeeeeeeeee......hhhhhhhhh...............hhhhh...eeeeeeeee....eeeeeeeeeee..eeeeeeeeeee............eeee..eeeeeeee..eeeeeeeeeeee....eeeeeeeeeeee..........eeeeeeeeeeee.....eeeeeeeeeee...... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ljb D   1 MSAIKPDMKINLRMEGNVNGHHFVIDGDGTGKPFEGKQSMDLEVKEGGPLPFAFDILTTAFhNRVFAEYPDHIQDYFKQSFPKGYSWERSLTFEDGGICIARNDITMEGDTFYNKVRFHGVNFPANGPVMQKKTLKWEPSTEKMYVRDGVLTGDITMALLLEGNAHYRCDSRTTYKAKEKGVKLPGYHLVDHCIEILSHDKDYNKVKLYEHAVAHSGLPDN 223
                                    10        20        30        40        50        60||      72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222 
                                                                                       61|                                                                                                                                                               
                                                                                        64-CR8

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: automated matches (66)

Protein domain: automated matches (66)

Lobophyllia hemprichii [TaxId: 46758] (12)

1a	d4ljba_	A:
1b	d4ljbb_	B:
1c	d4ljbc_	C:
1d	d4ljbd_	D:

(no "CATH Domain" information available for 4LJB)

(no "Pfam Domain" information available for 4LJB)

Asymmetric/Biological Unit(hide GO term definitions)

Asymmetric/Biological Unit
	Complete Structure
		Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
		WebMol \| AstexViewer[tm]@PDBe (Java Applets, require no local installation except for Java; loading may be slow)
		STRAP (Java WebStart application, automatic local installation, requires Java; full application with system access!)
		RasMol (require local installation)
		Molscript (VRML) (requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)

	Ligands, Modified Residues, Ions
		CR8	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		SO3	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		SO4	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]
		AC2	[ RasMol ]	+environment [ RasMol ]
		AC3	[ RasMol ]	+environment [ RasMol ]
		AC4	[ RasMol ]	+environment [ RasMol ]
		AC5	[ RasMol ]	+environment [ RasMol ]
		AC6	[ RasMol ]	+environment [ RasMol ]
		AC7	[ RasMol ]	+environment [ RasMol ]
		AC8	[ RasMol ]	+environment [ RasMol ]
		AC9	[ RasMol ]	+environment [ RasMol ]
		BC1	[ RasMol ]	+environment [ RasMol ]
		BC2	[ RasMol ]	+environment [ RasMol ]
		BC3	[ RasMol ]	+environment [ RasMol ]
		BC4	[ RasMol ]	+environment [ RasMol ]
		BC5	[ RasMol ]	+environment [ RasMol ]
		BC6	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
		Gly A:48 - Pro A:49	[ RasMol ]
		Gly B:48 - Pro B:49	[ RasMol ]
		Gly C:48 - Pro C:49	[ RasMol ]
		Gly D:48 - Pro D:49	[ RasMol ]
		Leu A:220 - Pro A:221	[ RasMol ]
		Leu B:220 - Pro B:221	[ RasMol ]
		Leu C:220 - Pro C:221	[ RasMol ]
		Leu D:220 - Pro D:221	[ RasMol ]
		Phe A:83 - Pro A:84	[ RasMol ]
		Phe B:83 - Pro B:84	[ RasMol ]
		Phe C:83 - Pro C:84	[ RasMol ]
		Phe D:83 - Pro D:84	[ RasMol ]

Jmol
	protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick [ Asym./Biol. Unit PNG format \| Asym./Biol. Unit - sites PNG format ](automatic orientation, automatically generated)
Molscript
	protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick [ mono PDF format \| stereo PDF format ](default orientation, automatically generated)

Access by PDB/NDB ID
	4ljb
		Family and Domain Information	:	ProDom \| SYSTERS
		General Structural Information	:	GlycoscienceDB \| MMDB \| NDB \| OCA \| PDB \| PDBe \| PDBj \| PDBsum \| PDBWiki \| PQS \| PROTEOPEDIA
		Orientation in Membranes	:	OPM
		Protein Surface	:	SURFACE
		Secondary Structure	:	DSSP (structure derived) \| HSSP (homology derived)
		Structural Genomics	:	GeneCensus
		Structural Neighbours	:	CE \| VAST
		Structure Classification	:	CATH \| Dali \| SCOP
		Validation and Original Data	:	BMRB Data View \| BMRB Restraints Grid \| EDS \| PROCHECK \| RECOORD \| WHAT_CHECK

Access by UniProt ID/Accession number
	Q5S6Z9_LOBHE \| Q5S6Z9
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/TrEMBL

Access by Enzyme Classificator (EC Number)
	(no 'Enzyme Classificator' available)
		General Enzyme Information	:	BRENDA \| EC-PDB \| Enzyme \| IntEnz
		Pathway	:	KEGG \| MetaCyc

Access by Disease Identifier (MIM ID)
	(no 'MIM ID' available)
		Disease Information	:	OMIM

Access by GenAge ID
	(no 'GenAge ID' available)
		Age Related Information	:	GenAge

Access by PDB/NDB ID
		Domain Information	:	XDom
		Interatomic Contacts of Structural Units	:	CSU
		Ligand-protein Contacts	:	LPC
		Protein Cavities	:	castP
		Sequence and Secondary Structure	:	PDBCartoon
		Structure Alignment	:	STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
		Structure and Sequence Browser	:	STING

Access by UniProt ID/Accession number
	Q5S6Z9_LOBHE \| Q5S6Z9
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

2vvh	CRYSTAL STRUCTURE OF IRISFP IN ITS GREEN STATE (CHROMOPHORE IN CIS CONFORMATION)
2vvi	CRYSTAL STRUCTURE OF IRISFP IN ITS DARK STATE (CHROMOPHORE IN TRANS CONFORMATION)
2vvj	CRYSTAL STRUCTURE OF IRISFP IN ITS RED STATE(CHROMOPHORE IN CIS CONFORMATION)
3tmr	CRYSTAL STRUCTURE OF NATIVE IRISFP (LOW X-RAY DOSE, PLANAR CHROMOPHORE)
3tmt	CRYSTAL STRUCTURE OF IRISFP IN ITS BLINKED STATE (DISTORTED CHROMOPHORE)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 20)

Sites (15, 15)

SS Bonds (0, 0)

Cis Peptide Bonds (12, 12)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (1, 4)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (2, 2)

Visualization

Interactive Views

Still Images

Databases and Analysis Tools

Databases

Analysis Tools

Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File