1TEF - JenaLib

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Title :   CRYSTAL STRUCTURE OF THE SPINACH PLASTOCYANIN MUTANTS G8D/K30C/T69C AND K30C/T69C- A STUDY OF THE EFFECT ON CRYSTAL PACKING AND THERMOSTABILITY FROM THE INTRODUCTION OF A NOVEL DISULFIDE BOND

Authors :   M. Okvist, F. Jacobson, H. Jansson, O. Hansson, L. Sjolin

Date :   25 May 04 (Deposition) - 01 Nov 05 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.90

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

Keywords :   Plastocyanin, Disulfide Bond, Mutant, Blue Copper Protein, Photosynthesis (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. Okvist, F. Jacobson, H. Jansson, O. Hansson, L. Sjolin
Novel Disulfide Bonds Effect The Thermostability Of Plastocyanin. Crystal Structures Of The Triple Plastocyanin Mutant G8D/K30C/T69C And The Double Plastocyanin Mutant K30C/T69C From Spinach At 1. 90 And 1. 96 Resolution, Respectively.
To Be Published
PubMed: search
(for further references see the PDB file header)

Molecule 1 - PLASTOCYANIN, CHLOROPLAST
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PUG101TR
	Expression System Strain	:	RV308
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	PETE
	Mutation	:	YES
	Organism Common	:	SPINACH
	Organism Scientific	:	SPINACIA OLERACEA
	Organism Taxid	:	3562

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 3)

No.	Name	Count	Type	Full Name
1	CL	1	Ligand/Ion	CHLORIDE ION
2	CU	2	Ligand/Ion	COPPER (II) ION

Biological Unit 1 (0, 0)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION
2	CU	-1	Ligand/Ion	COPPER (II) ION

Biological Unit 2 (0, 0)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION
2	CU	-1	Ligand/Ion	COPPER (II) ION

Asymmetric Unit (3, 3)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HIS A:37 , CYS A:84 , HIS A:87 , MET A:92	BINDING SITE FOR RESIDUE CU A 401
2	AC2	SOFTWARE	HIS B:37 , CYS B:84 , HIS B:87 , MET B:92	BINDING SITE FOR RESIDUE CU B 402
3	AC3	SOFTWARE	ASP A:51 , HOH A:424	BINDING SITE FOR RESIDUE CL A 403

Asymmetric Unit

No.	Residues
1	A:30	-	A:69
2	B:30	-	B:69

Asymmetric Unit

No.	Residues
1	Leu A:15	-	Pro A:16
2	Phe A:35	-	Pro A:36
3	Leu B:15	-	Pro B:16
4	Phe B:35	-	Pro B:36

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

Asymmetric Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	COPPER_BLUE	PS00196	Type-1 copper (blue) proteins signature.	PLAS_SPIOL	147-161	2	A:78-92 B:78-92

Biological Unit 1 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	COPPER_BLUE	PS00196	Type-1 copper (blue) proteins signature.	PLAS_SPIOL	147-161	1	A:78-92 -

Biological Unit 2 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	COPPER_BLUE	PS00196	Type-1 copper (blue) proteins signature.	PLAS_SPIOL	147-161	1	- B:78-92

(no "Exon" information available for 1TEF)

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:99
 aligned with PLAS_SPIOL | P00289 from UniProtKB/Swiss-Prot  Length:168

    Alignment length:99
                                    79        89        99       109       119       129       139       149       159         
           PLAS_SPIOL    70 VEVLLGGGDGSLAFLPGDFSVASGEEIVFKNNAGFPHNVVFDEDEIPSGVDAAKISMSEEDLLNAPGETYKVTLTEKGTYKFYCSPHQGAGMVGKVTVN 168
               SCOP domains d1tefa_ A: Plastocyanin                                                                             SCOP domains
               CATH domains 1tefA00 A:1-99 Cupredoxins -  blue copper proteins                                                  CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee........ee..eeeee...eeeeee........ee.........hhhhhh............eeeee....eeeeee...hhhhh.eeeeeee Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------COPPER_BLUE    ------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------- Transcript
                 1tef A   1 VEVLLGGDDGSLAFLPGDFSVASGEEIVFCNNAGFPHNVVFDEDEIPSGVDAAKISMSEEDLLNAPGECYKVTLTEKGTYKFYCSPHQGAGMVGKVTVN  99
                                    10        20        30        40        50        60        70        80        90

Chain B from PDB  Type:PROTEIN  Length:99
 aligned with PLAS_SPIOL | P00289 from UniProtKB/Swiss-Prot  Length:168

    Alignment length:99
                                    79        89        99       109       119       129       139       149       159         
           PLAS_SPIOL    70 VEVLLGGGDGSLAFLPGDFSVASGEEIVFKNNAGFPHNVVFDEDEIPSGVDAAKISMSEEDLLNAPGETYKVTLTEKGTYKFYCSPHQGAGMVGKVTVN 168
               SCOP domains d1tefb_ B: Plastocyanin                                                                             SCOP domains
               CATH domains 1tefB00 B:1-99 Cupredoxins -  blue copper proteins                                                  CATH domains
           Pfam domains (1) Copper-bind-1tefB01 B:1-99                                                                          Pfam domains (1)
           Pfam domains (2) Copper-bind-1tefB02 B:1-99                                                                          Pfam domains (2)
         Sec.struct. author .eeee........ee..eeee....eeeeee........ee.........hhhhhh............eeeee....eeeeee.hhhhhhh.eeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------COPPER_BLUE    ------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------- Transcript
                 1tef B   1 VEVLLGGDDGSLAFLPGDFSVASGEEIVFCNNAGFPHNVVFDEDEIPSGVDAAKISMSEEDLLNAPGECYKVTLTEKGTYKFYCSPHQGAGMVGKVTVN  99
                                    10        20        30        40        50        60        70        80        90

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 beta proteins (24004)

Fold: Cupredoxin-like (545)

Superfamily: Cupredoxins (543)

Family: Plastocyanin/azurin-like (241)

Protein domain: Plastocyanin (56)

Spinach (Spinacia oleracea) [TaxId: 3562] (4)

1a	d1tefa_	A:
1b	d1tefb_	B:

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Beta (13760)

Architecture: Sandwich (5577)

Topology: Immunoglobulin-like (3897)

Homologous Superfamily: Cupredoxins - blue copper proteins (420)

Spinach (Spinacia oleracea) (7)

1a	1tefA00	A:1-99
1b	1tefB00	B:1-99

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: CU_oxidase (192)

Family: Copper-bind (82)

Spinacia oleracea (Spinach) (5)

1a	Copper-bind-1tefB01	B:1-99
1b	Copper-bind-1tefB02	B:1-99

Asymmetric Unit(hide GO term definitions)

Chain A,B (PLAS_SPIOL | P00289)

molecular function
	GO:0005507	copper ion binding	Interacting selectively and non-covalently with copper (Cu) ions.
	GO:0009055	electron carrier activity	Any molecular entity that serves as an electron acceptor and electron donor in an electron transport chain. An electron transport chain is a process in which a series of electron carriers operate together to transfer electrons from donors to any of several different terminal electron acceptors to generate a transmembrane electrochemical gradient.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
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.
cellular component
	GO:0009507	chloroplast	A chlorophyll-containing plastid with thylakoids organized into grana and frets, or stroma thylakoids, and embedded in a stroma.
	GO:0009535	chloroplast thylakoid membrane	The pigmented membrane of a chloroplast thylakoid. An example of this component is found in Arabidopsis thaliana.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
	GO:0009536	plastid	Any member of a family of organelles found in the cytoplasm of plants and some protists, which are membrane-bounded and contain DNA. Plant plastids develop from a common type, the proplastid.
	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.

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1teg	DOUBLE PLASTOCYANIN MUTANT K30C/T69C

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Ligands, Modified Residues, Ions (2, 3)

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Cis Peptide Bonds (4, 4)

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