2PY8 - JenaLib

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Biological Unit 3 (Jmol Viewer)

Title :   RBCX

Authors :   S. Tanaka, M. R. Sawaya, C. A. Kerfeld, T. O. Yeates

Date :   15 May 07 (Deposition) - 09 Oct 07 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.45

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

Keywords :   All Helical Fold, Chaperone (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. Tanaka, M. R. Sawaya, C. A. Kerfeld, T. O. Yeates
Structure Of The Rubisco Chaperone Rbcx From Synechocystis Sp. Pcc6803.
Acta Crystallogr. , Sect. D V. 63 1109 2007
PubMed-ID: 17881829 | Reference-DOI: 10.1107/S090744490704228X

Molecule 1 - HYPOTHETICAL PROTEIN RBCX
	Chains	:	A, B, C, D
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET22B
	Expression System Strain	:	BL21-GOLD (DE3)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	RBCX
	Organism Scientific	:	SYNECHOCYSTIS SP. PCC 6803
	Organism Taxid	:	1148
	Strain	:	PCC6803

		1	2	3	4
Asymmetric Unit	:	A	B	C	D
Biological Unit 1 (1x)	:		B	C
Biological Unit 2 (2x)	:	A
Biological Unit 3 (2x)	:				D

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 4)

No.	Name	Count	Type	Full Name
1	CL	1	Ligand/Ion	CHLORIDE ION
2	PE4	3	Ligand/Ion	2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL

Biological Unit 1 (1, 2)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION
2	PE4	2	Ligand/Ion	2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL

Biological Unit 2 (0, 0)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION
2	PE4	-1	Ligand/Ion	2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL

Biological Unit 3 (1, 2)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION
2	PE4	2	Ligand/Ion	2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ARG A:108 , THR A:112 , THR C:112	BINDING SITE FOR RESIDUE CL A 500
2	AC2	SOFTWARE	VAL B:13 , PE4 B:602 , VAL C:13 , TYR C:17 , TYR C:20 , ILE C:50 , GLN C:51 , HOH C:621 , HOH C:632 , HOH C:633	BINDING SITE FOR RESIDUE PE4 C 601
3	AC3	SOFTWARE	VAL B:13 , SER B:16 , TYR B:17 , TYR B:20 , ILE B:50 , GLN B:51 , PE4 C:601 , HOH C:632	BINDING SITE FOR RESIDUE PE4 B 602
4	AC4	SOFTWARE	TYR A:17 , TYR A:20 , GLN A:51 , TYR D:20 , GLN D:51	BINDING SITE FOR RESIDUE PE4 D 603

(no "SS Bond" information available for 2PY8)

Asymmetric Unit

No.	Residues
1	Phe A:119	-	Pro A:120
2	Phe C:119	-	Pro C:120

(no "SAP(SNP)/Variant" information available for 2PY8)

(no "PROSITE Motif" information available for 2PY8)

(no "Exon" information available for 2PY8)

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:120
 aligned with Q55670_SYNY3 | Q55670 from UniProtKB/TrEMBL  Length:138

    Alignment length:120
                                    13        23        33        43        53        63        73        83        93       103       113       123
         Q55670_SYNY3     4 QTKHIAQATVKVLQSYLTYQAVLRIQSELGETNPPQAIWLNQYLASHSIQNGETFLTELLDENKELVLRILAVREDIAESVLDFLPGMTRNSLAESNIAHRRHLLERLTRTVAEVDNFPS 123
               SCOP domains d2py8a1 A:2-121 RuBisCo chaperone RbcX                                                                                   SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------ Transcript
                 2py8 A   2 QTKHIAQATVKVLQSYLTYQAVLRIQSELGETNPPQAIWLNQYLASHSIQNGETFLTELLDENKELVLRILAVREDIAESVLDFLPGMTRNSLAESNIAHRRHLLERLTRTVAEVDNFPS 121
                                    11        21        31        41        51        61        71        81        91       101       111       121

Chain B from PDB  Type:PROTEIN  Length:114
 aligned with Q55670_SYNY3 | Q55670 from UniProtKB/TrEMBL  Length:138

    Alignment length:114
                                    13        23        33        43        53        63        73        83        93       103       113    
         Q55670_SYNY3     4 QTKHIAQATVKVLQSYLTYQAVLRIQSELGETNPPQAIWLNQYLASHSIQNGETFLTELLDENKELVLRILAVREDIAESVLDFLPGMTRNSLAESNIAHRRHLLERLTRTVAE 117
               SCOP domains d2py8b_ B: RuBisCo chaperone RbcX                                                                                  SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh...hhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------ Transcript
                 2py8 B   2 QTKHIAQATVKVLQSYLTYQAVLRIQSELGETNPPQAIWLNQYLASHSIQNGETFLTELLDENKELVLRILAVREDIAESVLDFLPGMTRNSLAESNIAHRRHLLERLTRTVAE 115
                                    11        21        31        41        51        61        71        81        91       101       111

Chain C from PDB  Type:PROTEIN  Length:123
 aligned with Q55670_SYNY3 | Q55670 from UniProtKB/TrEMBL  Length:138

    Alignment length:123
                                    13        23        33        43        53        63        73        83        93       103       113       123   
         Q55670_SYNY3     4 QTKHIAQATVKVLQSYLTYQAVLRIQSELGETNPPQAIWLNQYLASHSIQNGETFLTELLDENKELVLRILAVREDIAESVLDFLPGMTRNSLAESNIAHRRHLLERLTRTVAEVDNFPSETS 126
               SCOP domains d2py8c_ C: RuBisCo chaperone RbcX                                                                                           SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhh..hhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------- Transcript
                 2py8 C   2 QTKHIAQATVKVLQSYLTYQAVLRIQSELGETNPPQAIWLNQYLASHSIQNGETFLTELLDENKELVLRILAVREDIAESVLDFLPGMTRNSLAESNIAHRRHLLERLTRTVAEVDNFPSETS 124
                                    11        21        31        41        51        61        71        81        91       101       111       121

Chain D from PDB  Type:PROTEIN  Length:103
 aligned with Q55670_SYNY3 | Q55670 from UniProtKB/TrEMBL  Length:138

    Alignment length:103
                                    13        23        33        43        53        63        73        83        93       103   
         Q55670_SYNY3     4 QTKHIAQATVKVLQSYLTYQAVLRIQSELGETNPPQAIWLNQYLASHSIQNGETFLTELLDENKELVLRILAVREDIAESVLDFLPGMTRNSLAESNIAHRRH 106
               SCOP domains d2py8d_ D: RuBisCo chaperone RbcX                                                                       SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) RcbX-2py8D01 D:2-104                                                                                    Pfam domains (1)
           Pfam domains (2) RcbX-2py8D02 D:2-104                                                                                    Pfam domains (2)
           Pfam domains (3) RcbX-2py8D03 D:2-104                                                                                    Pfam domains (3)
           Pfam domains (4) RcbX-2py8D04 D:2-104                                                                                    Pfam domains (4)
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhh..hhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------- Transcript
                 2py8 D   2 QTKHIAQATVKVLQSYLTYQAVLRIQSELGETNPPQAIWLNQYLASHSIQNGETFLTELLDENKELVLRILAVREDIAESVLDFLPGMTRNSLAESNIAHRRH 104
                                    11        21        31        41        51        61        71        81        91       101

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: All alpha proteins (14657)

Fold: RbcX-like (15)

Superfamily: RbcX-like (15)

Family: RbcX-like (13)

Protein domain: RuBisCo chaperone RbcX (13)

Synechocystis sp. PCC 6803 [TaxId: 1148] (1)

1a	d2py8a1	A:2-121
1b	d2py8b_	B:
1c	d2py8c_	C:
1d	d2py8d_	D:

(no "CATH Domain" information available for 2PY8)

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: no clan defined [family: RcbX] (13)

Family: RcbX (13)

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

1a	RcbX-2py8D01	D:2-104
1b	RcbX-2py8D02	D:2-104
1c	RcbX-2py8D03	D:2-104
1d	RcbX-2py8D04	D:2-104

Asymmetric Unit(hide GO term definitions)

(no "Gene Ontology" information available for 2PY8)

Asymmetric Unit
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Description

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Ligands, Modified Residues, Ions (2, 4)

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SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

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