3MG3 - JenaLib

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Biological Unit 3 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF THE ORANGE CAROTENOID PROTEIN R155L MUTANT FROM CYANOBACTERIA SYNECHOCYSTIS SP. PCC 6803

Authors :   A. Wilson, J. Kinney, P. H. Zwart, C. Punginelli, S. D'Haen, F. Perreau, M. G. Klein, D. Kirilovsky, C. A. Kerfeld

Date :   05 Apr 10 (Deposition) - 14 Apr 10 (Release) - 11 Aug 10 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.70

Chains :   Asym. Unit : A,B
Biol. Unit 1: A,B  (1x)
Biol. Unit 2: A  (1x)
Biol. Unit 3: B  (1x)

Keywords :   Carotenoid Binding Protein, Echinone, Phycobilisome (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   A. Wilson, J. N. Kinney, P. H. Zwart, C. Punginelli, S. D'Haene, F. Perreau, M. G. Klein, D. Kirilovsky, C. A. Kerfeld
Structural Determinants Underlying Photoprotection In The Photoactive Orange Carotenoid Protein Of Cyanobacteria.
J. Biol. Chem. V. 285 18364 2010
PubMed-ID: 20368334 | Reference-DOI: 10.1074/JBC.M110.115709
(for further references see the PDB file header)

Molecule 1 - ORANGE CAROTENOID-BINDING PROTEIN
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Gene	:	SLR1963
	Mutation	:	YES
	Organism Scientific	:	SYNECHOCYSTIS SP.
	Organism Taxid	:	1148
	Strain	:	PCC 6803
	Synonym	:	OCP

		1	2
Asymmetric Unit	:	A	B
Biological Unit 1 (1x)	:	A	B
Biological Unit 2 (1x)	:	A
Biological Unit 3 (1x)	:		B

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 9)

No.	Name	Count	Type	Full Name
1	ECH	2	Ligand/Ion	BETA,BETA-CAROTEN-4-ONE
2	GOL	7	Ligand/Ion	GLYCEROL

Biological Unit 1 (2, 9)

No.	Name	Count	Type	Full Name
1	ECH	2	Ligand/Ion	BETA,BETA-CAROTEN-4-ONE
2	GOL	7	Ligand/Ion	GLYCEROL

Biological Unit 2 (2, 4)

No.	Name	Count	Type	Full Name
1	ECH	1	Ligand/Ion	BETA,BETA-CAROTEN-4-ONE
2	GOL	3	Ligand/Ion	GLYCEROL

Biological Unit 3 (2, 5)

No.	Name	Count	Type	Full Name
1	ECH	1	Ligand/Ion	BETA,BETA-CAROTEN-4-ONE
2	GOL	4	Ligand/Ion	GLYCEROL

Asymmetric Unit (9, 9)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ILE A:40 , TYR A:44 , TRP A:110 , TYR A:111 , GLY A:114 , ILE A:151 , THR A:152 , VAL A:158 , TYR A:201 , LEU A:205 , CYS A:245 , VAL A:273 , MET A:284 , TRP A:288 , ILE A:303 , GOL A:326	BINDING SITE FOR RESIDUE ECH A 351
2	AC2	SOFTWARE	ILE B:40 , TYR B:44 , LEU B:107 , TRP B:110 , TYR B:111 , GLY B:114 , ILE B:151 , THR B:152 , VAL B:158 , TYR B:201 , LEU B:205 , CYS B:245 , VAL B:273 , MET B:284 , TRP B:288 , ILE B:303 , GOL B:326	BINDING SITE FOR RESIDUE ECH B 351
3	AC3	SOFTWARE	ALA A:55 , PRO A:56 , GLY A:57 , GLU A:174 , PRO A:276 , TRP A:277 , HOH A:1011 , HOH A:1088 , HOH A:1174 , HOH A:1376	BINDING SITE FOR RESIDUE GOL A 324
4	AC4	SOFTWARE	ASN A:104 , GLU A:244 , TRP A:277 , GOL A:326 , HOH A:1012 , HOH A:1019	BINDING SITE FOR RESIDUE GOL A 325
5	AC5	SOFTWARE	ALA B:55 , PRO B:56 , GLY B:57 , GLU B:174 , PRO B:276 , TRP B:277 , HOH B:1010 , HOH B:1059 , HOH B:1077 , HOH B:1171	BINDING SITE FOR RESIDUE GOL B 324
6	AC6	SOFTWARE	ASN B:104 , GLU B:244 , TRP B:277 , GOL B:326 , HOH B:1009 , HOH B:1023	BINDING SITE FOR RESIDUE GOL B 325
7	AC7	SOFTWARE	PRO A:225 , PRO A:226 , GLN A:228 , PHE A:240 , GOL A:325 , ECH A:351 , HOH A:1184 , HOH A:1462 , HOH A:1646	BINDING SITE FOR RESIDUE GOL A 326
8	AC8	SOFTWARE	ASN B:156 , PRO B:225 , PRO B:226 , GLN B:228 , PHE B:240 , GOL B:325 , ECH B:351 , HOH B:1226 , HOH B:1485	BINDING SITE FOR RESIDUE GOL B 326
9	AC9	SOFTWARE	SER A:132 , ASN A:134 , ARG B:9 , GLY B:10 , ILE B:11 , PHE B:12 , PRO B:13 , THR B:15 , ARG B:289 , HOH B:1035 , HOH B:1097 , HOH B:1134 , HOH B:1469	BINDING SITE FOR RESIDUE GOL B 327

(no "SS Bond" information available for 3MG3)

(no "Cis Peptide Bond" information available for 3MG3)

(no "SAP(SNP)/Variant" information available for 3MG3)

Asymmetric Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	OCP_N	PS51773	Orange carotenoid protein (OCP) N-terminal domain profile.	OCP_SYNY3	18-169	2	A:18-164 B:18-164

Biological Unit 1 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	OCP_N	PS51773	Orange carotenoid protein (OCP) N-terminal domain profile.	OCP_SYNY3	18-169	2	A:18-164 B:18-164

Biological Unit 2 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	OCP_N	PS51773	Orange carotenoid protein (OCP) N-terminal domain profile.	OCP_SYNY3	18-169	1	A:18-164 -

Biological Unit 3 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	OCP_N	PS51773	Orange carotenoid protein (OCP) N-terminal domain profile.	OCP_SYNY3	18-169	1	- B:18-164

(no "Exon" information available for 3MG3)

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:304
 aligned with OCP_SYNY3 | P74102 from UniProtKB/Swiss-Prot  Length:317

    Alignment length:309
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303         
            OCP_SYNY3     4 TIDSARGIFPNTLAADVVPATIARFSQLNAEDQLALIWFAYLEMGKTLTIAAPGAASMQLAENALKEIQAMGPLQQTQAMCDLANRADTPLCRTYASWSPNIKLGFWYRLGELMEQGFVAPIPAGYQLSANANAVLATIQGLESGQQITVLRNAVVDMGFTAGKDGKRIAEPVVPPQDTASRTKVSIEGVTNATVLNYMDNLNANDFDTLIELFTSDGALQPPFQRPIVGKENVLRFFREECQNLKLIPERGVTEPAEDGFTQIKVTGKVQTPWFGGNVGMNIAWRFLLNPEGKIFFVAIDLLASPKEL 312
               SCOP domains d3mg3a1 A:4-173 automated matches                                                                                                                                         d3mg3a2 A:174-312 automated matches                                                                                                         SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhh............hhhhhhhhhhhhh.hhhhhhhhhhhhhhh....-----...........hhhhh.........hhhhhhhhhhhhh.hhhhhhh.eeeeeeee......eehhhhhhhhhhhhh...eeeeeeeeeee.hhh.eeeeeeeeee...hhhhh.eeeeeeeee.....eeeeeeee..hhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------OCP_N  PDB: A:18-164 UniProt: 18-169                                                                                                                    ----------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3mg3 A   4 TIDSARGIFPNTLAADVVPATIARFSQLNAEDQLALIWFAYLEMGKTLTIAAPGAASMQLAENALKEIQAMGPLQQTQAMCDLANRADTPLCRTYASWSPNIKLGFWYRLGELMEQGFVAPIPAGYQLSANANAVLATIQGLESGQQITVLLNAVVDMGFT-----KRIAEPVVPPQDTASRTKVSIEGVTNATVLNYMDNLNANDFDTLIELFTSDGALQPPFQRPIVGKENVLRFFREECQNLKLIPERGVTEPAEDGFTQIKVTGKVQTPWFGGNVGMNIAWRFLLNPEGKIFFVAIDLLASPKEL 312
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163|     |173       183       193       203       213       223       233       243       253       263       273       283       293       303         
                                                                                                                                                                                          164   170

Chain B from PDB  Type:PROTEIN  Length:304
 aligned with OCP_SYNY3 | P74102 from UniProtKB/Swiss-Prot  Length:317

    Alignment length:309
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302         
            OCP_SYNY3     3 FTIDSARGIFPNTLAADVVPATIARFSQLNAEDQLALIWFAYLEMGKTLTIAAPGAASMQLAENALKEIQAMGPLQQTQAMCDLANRADTPLCRTYASWSPNIKLGFWYRLGELMEQGFVAPIPAGYQLSANANAVLATIQGLESGQQITVLRNAVVDMGFTAGKDGKRIAEPVVPPQDTASRTKVSIEGVTNATVLNYMDNLNANDFDTLIELFTSDGALQPPFQRPIVGKENVLRFFREECQNLKLIPERGVTEPAEDGFTQIKVTGKVQTPWFGGNVGMNIAWRFLLNPEGKIFFVAIDLLASPKE 311
               SCOP domains d3mg3b1 B:3-173 automated matches                                                                                                                                          d3mg3b2 B:174-311 automated matches                                                                                                        SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -Carot_N-3mg3B03 B:4-164                                                                                                                                          ----------------------------NTF2-3mg3B01 B:193-308                                                                                              --- Pfam domains (1)
           Pfam domains (2) -Carot_N-3mg3B04 B:4-164                                                                                                                                          ----------------------------NTF2-3mg3B02 B:193-308                                                                                              --- Pfam domains (2)
         Sec.struct. author .hhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhh............hhhhhhhhhhhhh.hhhhhhhhhhhhhhh....-----...........hhhhh.........hhhhhhhhhhhhh.hhhhhhh.eeeeeeee......eehhhhhhhhhhhhh...eeeeeeeeeee.hhh.eeeeeeeeee...hhhhh.eeeeeeeee.....eeeeeeee...... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------OCP_N  PDB: B:18-164 UniProt: 18-169                                                                                                                    ---------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3mg3 B   3 FTIDSARGIFPNTLAADVVPATIARFSQLNAEDQLALIWFAYLEMGKTLTIAAPGAASMQLAENALKEIQAMGPLQQTQAMCDLANRADTPLCRTYASWSPNIKLGFWYRLGELMEQGFVAPIPAGYQLSANANAVLATIQGLESGQQITVLLNAVVDMGFT-----KRIAEPVVPPQDTASRTKVSIEGVTNATVLNYMDNLNANDFDTLIELFTSDGALQPPFQRPIVGKENVLRFFREECQNLKLIPERGVTEPAEDGFTQIKVTGKVQTPWFGGNVGMNIAWRFLLNPEGKIFFVAIDLLASPKE 311
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162 |     172       182       192       202       212       222       232       242       252       262       272       282       292       302         
                                                                                                                                                                                           164   170

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 '\|'

(no "CATH Domain" information available for 3MG3, only for superseded entry 3I1X replaced by 3MG3)

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: NTF2 (66)

Family: NTF2 (30)

Synechocystis sp. (strain ATCC 27184 / PCC 6803 / N-1) (3)

1a	NTF2-3mg3B01	B:193-308
1b	NTF2-3mg3B02	B:193-308

Clan: no clan defined [family: Carot_N] (3)

Family: Carot_N (3)

Synechocystis sp. (strain ATCC 27184 / PCC 6803 / N-1) (3)

2a	Carot_N-3mg3B03	B:4-164
2b	Carot_N-3mg3B04	B:4-164

Asymmetric Unit(hide GO term definitions)

Chain A,B (OCP_SYNY3 | P74102)

molecular function
	GO:0031404	chloride ion binding	Interacting selectively and non-covalently with chloride ions (Cl-).
	GO:0009881	photoreceptor activity	The function of absorbing and responding to incidental electromagnetic radiation, particularly visible light. The response may involve a change in conformation.
biological process
	GO:0016037	light absorption	The reception of a photon by a cell.
	GO:0018298	protein-chromophore linkage	The covalent or noncovalent attachment of a chromophore to a protein.
	GO:0050896	response to stimulus	Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus. The process begins with detection of the stimulus and ends with a change in state or activity or the cell or organism.
	GO:0007165	signal transduction	The cellular process in which a signal is conveyed to trigger a change in the activity or state of a cell. Signal transduction begins with reception of a signal (e.g. a ligand binding to a receptor or receptor activation by a stimulus such as light), or for signal transduction in the absence of ligand, signal-withdrawal or the activity of a constitutively active receptor. Signal transduction ends with regulation of a downstream cellular process, e.g. regulation of transcription or regulation of a metabolic process. Signal transduction covers signaling from receptors located on the surface of the cell and signaling via molecules located within the cell. For signaling between cells, signal transduction is restricted to events at and within the receiving cell.
	GO:0006810	transport	The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter, pore or motor protein.
cellular component
	GO:0005622	intracellular	The living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
	GO:0030089	phycobilisome	Any of the granules, approximately 32 nm x 48 nm and consisting of highly aggregated phycobiliproteins, that are attached in arrays to the external face of a thylakoid membrane in algae of the phyla Cyanophyta and Rhodophyta, where they function as light-harvesting devices in photosynthesis. Excitation energy in the phycobilisome flows in the sequence: phycoerythrin, phycocyanin, allophycocyanin before passing to the antenna chlorophyll of photosystem II.
	GO:0009579	thylakoid	A membranous cellular structure that bears the photosynthetic pigments in plants, algae, and cyanobacteria. In cyanobacteria thylakoids are of various shapes and are attached to, or continuous with, the plasma membrane. In eukaryotes they are flattened, membrane-bounded disk-like structures located in the chloroplasts; in the chloroplasts of higher plants the thylakoids form dense stacks called grana. Isolated thylakoid preparations can carry out photosynthetic electron transport and the associated phosphorylation.
	GO:0042651	thylakoid membrane	The pigmented membrane of any thylakoid.

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	Cis Peptide Bonds
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	OCP_SYNY3 \| P74102	:	3mg1 3mg2 4xb4 4xb5 5tuw 5tux 5tv0

1m98	ORANGE CAROTENOID BINDING PROTEIN FROM ARTHIROSPIRA
3mg1	CRYSTAL STRUCTURE OF ORANGE CAROTENOID BINDING PROTEIN FROM SYNECHOCYSTIS SP. PCC 6803
3mg2	CRYSTAL STRUCTURE OF Y44S MUTANT OF SYNECHOCYSTIS ORANGE CAROTENOID BINDING PROTEIN

Description

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Ligands, Modified Residues, Ions (2, 9)

Sites (9, 9)

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