1CPC - JenaLib

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Biological Unit 6 (Jmol Viewer)

Title :   ISOLATION, CRYSTALLIZATION, CRYSTAL STRUCTURE ANALYSIS AND REFINEMENT OF CONSTITUTIVE C-PHYCOCYANIN FROM THE CHROMATICALLY ADAPTING CYANOBACTERIUM FREMYELLA DIPLOSIPHON AT 1.66 ANGSTROMS RESOLUTION

Authors :   M. Duerring, G. B. Schmidt, R. Huber

Date :   11 Oct 90 (Deposition) - 15 Jan 93 (Release) - 10 Apr 13 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.66

Chains :   Asym. Unit : A,B,K,L
Biol. Unit 1: A,B  (1x)
Biol. Unit 2: K,L  (1x)
Biol. Unit 3: A,B,K,L  (3x)
Biol. Unit 4: A,B  (3x)
Biol. Unit 5: K,L  (3x)
Biol. Unit 6: A,B,K,L  (1x)

Keywords :   Light Harvesting Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. Duerring, G. B. Schmidt, R. Huber
Isolation, Crystallization, Crystal Structure Analysis And Refinement Of Constitutive C-Phycocyanin From The Chromatically Adapting Cyanobacterium Fremyella Diplosiphon At 1. 66 A Resolution.
J. Mol. Biol. V. 217 577 1991
PubMed-ID: 1899708 | Reference-DOI: 10.1016/0022-2836(91)90759-Y

Molecule 1 - C-PHYCOCYANIN (ALPHA SUBUNIT)
	Chains	:	A, K
	Engineered	:	YES
	Organism Scientific	:	FREMYELLA DIPLOSIPHON
	Organism Taxid	:	1197

Molecule 2 - C-PHYCOCYANIN (BETA SUBUNIT)
	Chains	:	B, L
	Engineered	:	YES
	Organism Scientific	:	FREMYELLA DIPLOSIPHON
	Organism Taxid	:	1197

		1	2	3	4
Asymmetric Unit	:	A	B	K	L
Biological Unit 1 (1x)	:	A	B
Biological Unit 2 (1x)	:			K	L
Biological Unit 3 (3x)	:	A	B	K	L
Biological Unit 4 (3x)	:	A	B
Biological Unit 5 (3x)	:			K	L
Biological Unit 6 (1x)	:	A	B	K	L

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 8)

No.	Name	Count	Type	Full Name
1	CYC	6	Ligand/Ion	PHYCOCYANOBILIN
2	MEN	2	Mod. Amino Acid	N-METHYL ASPARAGINE

Biological Unit 1 (2, 4)

No.	Name	Count	Type	Full Name
1	CYC	3	Ligand/Ion	PHYCOCYANOBILIN
2	MEN	1	Mod. Amino Acid	N-METHYL ASPARAGINE

Biological Unit 2 (2, 4)

No.	Name	Count	Type	Full Name
1	CYC	3	Ligand/Ion	PHYCOCYANOBILIN
2	MEN	1	Mod. Amino Acid	N-METHYL ASPARAGINE

Biological Unit 3 (2, 24)

No.	Name	Count	Type	Full Name
1	CYC	18	Ligand/Ion	PHYCOCYANOBILIN
2	MEN	6	Mod. Amino Acid	N-METHYL ASPARAGINE

Biological Unit 4 (2, 12)

No.	Name	Count	Type	Full Name
1	CYC	9	Ligand/Ion	PHYCOCYANOBILIN
2	MEN	3	Mod. Amino Acid	N-METHYL ASPARAGINE

Biological Unit 5 (2, 12)

No.	Name	Count	Type	Full Name
1	CYC	9	Ligand/Ion	PHYCOCYANOBILIN
2	MEN	3	Mod. Amino Acid	N-METHYL ASPARAGINE

Biological Unit 6 (2, 8)

No.	Name	Count	Type	Full Name
1	CYC	6	Ligand/Ion	PHYCOCYANOBILIN
2	MEN	2	Mod. Amino Acid	N-METHYL ASPARAGINE

Asymmetric Unit (7, 7)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	VAL A:59 , PRO A:72 , ASN A:73 , PHE A:74 , ALA A:75 , GLY A:80 , LYS A:83 , CYS A:84 , ARG A:86 , ASP A:87 , TYR A:110 , TRP A:128 , HOH A:188 , HOH A:189 , HOH A:216 , HOH A:227 , ARG B:57 , ILE B:67 , THR B:77 , HOH B:202	BINDING SITE FOR RESIDUE CYC A 175
2	AC2	unknown	LEU B:122 , THR B:124	NULL
3	AC3	SOFTWARE	ALA B:75 , ARG B:80 , ALA B:83 , CYS B:84 , ARG B:86 , ASP B:87 , ILE B:90 , ARG B:110 , LEU B:115 , LEU B:122 , SER B:128 , HOH B:213	BINDING SITE FOR RESIDUE CYC B 176
4	AC4	SOFTWARE	PHE A:28 , ASN B:35 , LYS B:36 , ASP B:39 , VAL B:40 , GLY B:145 , ASP B:146 , ILE B:150 , THR B:151 , ARG B:152 , GLY B:153 , CYS B:155 , HOH B:192 , HOH B:195 , HOH B:234 , GLN K:33 , ASN K:57 , ASP K:147 , VAL K:150 , HOH K:214	BINDING SITE FOR RESIDUE CYC B 177
5	AC5	SOFTWARE	VAL K:59 , THR K:66 , PRO K:72 , ASN K:73 , PHE K:74 , ALA K:75 , LYS K:83 , CYS K:84 , ARG K:86 , ASP K:87 , TYR K:110 , PHE K:122 , TRP K:128 , TYR K:129 , HOH K:187 , HOH K:198 , HOH K:199 , HOH K:221 , HOH K:224 , ARG L:57 , ILE L:67 , THR L:77	BINDING SITE FOR RESIDUE CYC K 175
6	AC6	SOFTWARE	LEU L:66 , ARG L:80 , CYS L:84 , ARG L:86 , ASP L:87 , ILE L:90 , ARG L:110 , LEU L:115 , LEU L:122	BINDING SITE FOR RESIDUE CYC L 176
7	AC7	SOFTWARE	GLN A:33 , ASP A:147 , VAL A:150 , ASN L:35 , ASP L:39 , VAL L:40 , GLY L:145 , ASP L:146 , ILE L:150 , THR L:151 , ARG L:152 , GLY L:153 , CYS L:155 , HOH L:200 , HOH L:201 , HOH L:215	BINDING SITE FOR RESIDUE CYC L 177

(no "SS Bond" information available for 1CPC)

(no "Cis Peptide Bond" information available for 1CPC)

(no "SAP(SNP)/Variant" information available for 1CPC)

(no "PROSITE Motif" information available for 1CPC)

(no "Exon" information available for 1CPC)

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:162
 aligned with PHCA1_MICDP | P07122 from UniProtKB/Swiss-Prot  Length:162

    Alignment length:162
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160  
          PHCA1_MICDP     1 MKTPLTEAVAAADSQGRFLSSTEIQTAFGRFRQASASLAAAKALTEKASSLASGAANAVYSKFPYTTSQNGPNFASTQTGKDKCVRDIGYYLRMVTYCLVVGGTGPLDDYLIGGIAEINRTFDLSPSWYVEALKYIKANHGLSGDPAVEANSYIDYAINALS 162
               SCOP domains d1cpca_ A: Phycocyanin alpha subunit                                                                                                                               SCOP domains
               CATH domains 1cpcA00 A:1-174 Phycocyanins                                                                                                                                       CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhh..hhhhhhhhhh.hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1cpc A   1 MKTPLTEAVAAADSQGRFLSSTEIQTAFGRFRQASASLAAAKALTEKASSLASGAANAVYSKFPYTTSQNGPNFASTQTGKDKCVRDIGYYLRMVTYCLVVGGTGPLDDYLIGGIAEINRTFDLSPSWYVEALKYIKANHGLSGDPAVEANSYIDYAINALS 174
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140|      162       172  
                                                                                                                                                                     140|    150|             
                                                                                                                                                                      143     161

Chain B from PDB  Type:PROTEIN  Length:172
 aligned with PHCB1_MICDP | P07119 from UniProtKB/Swiss-Prot  Length:172

    Alignment length:172
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170  
          PHCB1_MICDP     1 MLDAFAKVVSQADARGEYLSGSQIDALSALVADGNKRMDVVNRITGNSSTIVANAARSLFAEQPQLIAPGGNAYTSRRMAACLRDMEIILRYVTYAIFAGDASVLDDRCLNGLKETYLALGTPGSSVAVGVQKMKDAALAIAGDTNGITRGDCASLMAEVASYFDKAASAVA 172
               SCOP domains d1cpcb_ B: Phycocyanin beta subunit                                                                                                                                          SCOP domains
               CATH domains 1cpcB00 B:1-174 Phycocyanins                                                                                                                                                 CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhh..hhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1cpc B   1 MLDAFAKVVSQADARGEYLSGSQIDALSALVADGNKRMDVVNRITGNSSTIVANAARSLFAEQPQLIAPGGnAYTSRRMAACLRDMEIILRYVTYAIFAGDASVLDDRCLNGLKETYLALGTPGSSVAVGVQKMKDAALAIAGDTNGITRGDCASLMAEVASYFDKAASAVA 174
                                    10        20        30        40        50        60        70 ||     82        92       102       112       122       132       142       152       162       172  
                                                                                                  72-MEN                                                                                                
                                                                                                   75

Chain K from PDB  Type:PROTEIN  Length:162
 aligned with PHCA1_MICDP | P07122 from UniProtKB/Swiss-Prot  Length:162

    Alignment length:162
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160  
          PHCA1_MICDP     1 MKTPLTEAVAAADSQGRFLSSTEIQTAFGRFRQASASLAAAKALTEKASSLASGAANAVYSKFPYTTSQNGPNFASTQTGKDKCVRDIGYYLRMVTYCLVVGGTGPLDDYLIGGIAEINRTFDLSPSWYVEALKYIKANHGLSGDPAVEANSYIDYAINALS 162
               SCOP domains d1cpck_ K: Phycocyanin alpha subunit                                                                                                                               SCOP domains
               CATH domains 1cpcK00 K:1-174 Phycocyanins                                                                                                                                       CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .................................................................................................................................................................. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1cpc K   1 MKTPLTEAVAAADSQGRFLSSTEIQTAFGRFRQASASLAAAKALTEKASSLASGAANAVYSKFPYTTSQNGPNFASTQTGKDKCVRDIGYYLRMVTYCLVVGGTGPLDDYLIGGIAEINRTFDLSPSWYVEALKYIKANHGLSGDPAVEANSYIDYAINALS 174
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140|      162       172  
                                                                                                                                                                     140|    150|             
                                                                                                                                                                      143     161

Chain L from PDB  Type:PROTEIN  Length:172
 aligned with PHCB1_MICDP | P07119 from UniProtKB/Swiss-Prot  Length:172

    Alignment length:172
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170  
          PHCB1_MICDP     1 MLDAFAKVVSQADARGEYLSGSQIDALSALVADGNKRMDVVNRITGNSSTIVANAARSLFAEQPQLIAPGGNAYTSRRMAACLRDMEIILRYVTYAIFAGDASVLDDRCLNGLKETYLALGTPGSSVAVGVQKMKDAALAIAGDTNGITRGDCASLMAEVASYFDKAASAVA 172
               SCOP domains d1cpcl_ L: Phycocyanin beta subunit                                                                                                                                          SCOP domains
               CATH domains 1cpcL00 L:1-174 Phycocyanins                                                                                                                                                 CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ............................................................................................................................................................................ Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1cpc L   1 MLDAFAKVVSQADARGEYLSGSQIDALSALVADGNKRMDVVNRITGNSSTIVANAARSLFAEQPQLIAPGGnAYTSRRMAACLRDMEIILRYVTYAIFAGDASVLDDRCLNGLKETYLALGTPGSSVAVGVQKMKDAALAIAGDTNGITRGDCASLMAEVASYFDKAASAVA 174
                                    10        20        30        40        50        60        70 ||     82        92       102       112       122       132       142       152       162       172  
                                                                                                  72-MEN                                                                                                
                                                                                                   75

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	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: All alpha proteins (14657)

Fold: Globin-like (1351)

Superfamily: Globin-like (1308)

Family: Phycocyanin-like phycobilisome proteins (65)

Protein domain: Phycocyanin alpha subunit (16)

Fremyella diplosiphon [TaxId: 1197] (1)

1a	d1cpca_	A:
1b	d1cpck_	K:

Protein domain: Phycocyanin beta subunit (15)

Fremyella diplosiphon [TaxId: 1197] (1)

2a	d1cpcb_	B:
2b	d1cpcl_	L:

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Alpha (13335)

Architecture: Orthogonal Bundle (10391)

Topology: Globin-like (786)

Homologous Superfamily: Phycocyanins (32)

Fremyella diplosiphon. Organism_taxid: 1197. (1)

1a	1cpcB00	B:1-174
1b	1cpcL00	L:1-174
1c	1cpcA00	A:1-174
1d	1cpcK00	K:1-174

(no "Pfam Domain" information available for 1CPC)

Asymmetric Unit(hide GO term definitions)

Chain A,K (PHCA1_MICDP | P07122)

biological process
	GO:0055114	oxidation-reduction process	A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.
	GO:0015979	photosynthesis	The synthesis by organisms of organic chemical compounds, especially carbohydrates, from carbon dioxide (CO2) using energy obtained from light rather than from the oxidation of chemical compounds.
	GO:0018298	protein-chromophore linkage	The covalent or noncovalent attachment of a chromophore to a protein.
cellular component
	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.

Chain B,L (PHCB1_MICDP | P07119)

biological process
	GO:0055114	oxidation-reduction process	A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.
	GO:0015979	photosynthesis	The synthesis by organisms of organic chemical compounds, especially carbohydrates, from carbon dioxide (CO2) using energy obtained from light rather than from the oxidation of chemical compounds.
	GO:0018298	protein-chromophore linkage	The covalent or noncovalent attachment of a chromophore to a protein.
cellular component
	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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Description

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Ligands, Modified Residues, Ions (2, 8)

Sites (7, 7)

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