2Q47 - JenaLib

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Title :   ENSEMBLE REFINEMENT OF THE PROTEIN CRYSTAL STRUCTURE OF A PUTATIVE PHOSPHOPROTEIN PHOSPHATASE FROM ARABIDOPSIS THALIANA GENE AT1G05000

Authors :   E. J. Levin, D. A. Kondrashov, G. E. Wesenberg, G. N. Phillips Jr. , Cent Eukaryotic Structural Genomics (Cesg)

Date :   31 May 07 (Deposition) - 19 Jun 07 (Release) - 10 Aug 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   3.30

Chains :   Asym. Unit : A,B  (16x)
Biol. Unit 1: A,B  (1x)
Biol. Unit 2: A,B  (3x)

Keywords :   Ensemble Refinement, Refinement Methodology Development, At1G05000, Phosphoprotein Phosphatase, Structural Genomics, Protein Structure Initiative, Psi, Center For Eukaryotic Structural Genomics, Cesg, Unknown Function (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   E. J. Levin, D. A. Kondrashov, G. E. Wesenberg, G. N. Phillips
Ensemble Refinement Of Protein Crystal Structures: Validation And Application.
Structure V. 15 1040 2007
PubMed-ID: 17850744 | Reference-DOI: 10.1016/J.STR.2007.06.019

Molecule 1 - PROBABLE TYROSINE-PROTEIN PHOSPHATASE AT1G05000
	Chains	:	A, B
	EC Number	:	3.1.3.48
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PVP-13
	Expression System Strain	:	B834(DE3)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	RESIDUES 52-202
	Gene	:	AT1G05000, T7A14.14
	Organism Common	:	THALE CRESS
	Organism Scientific	:	ARABIDOPSIS THALIANA
	Organism Taxid	:	3702
	Other Details	:	PQE DERIVATIVE
	Strain	:	CV. COLUMBIA

		1	2
Asymmetric Unit (16x)	:	A	B
Biological Unit 1 (1x)	:	A	B
Biological Unit 2 (3x)	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 10)

No.	Name	Count	Type	Full Name
1	MSE	6	Mod. Amino Acid	SELENOMETHIONINE
2	SO4	4	Ligand/Ion	SULFATE ION

Biological Unit 1 (2, 10)

No.	Name	Count	Type	Full Name
1	MSE	6	Mod. Amino Acid	SELENOMETHIONINE
2	SO4	4	Ligand/Ion	SULFATE ION

Biological Unit 2 (2, 10)

No.	Name	Count	Type	Full Name
1	MSE	6	Mod. Amino Acid	SELENOMETHIONINE
2	SO4	4	Ligand/Ion	SULFATE ION

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	CYS A:150 , LYS A:151 , ARG A:152 , GLY A:153 , LYS A:154 , HIS A:155 , ARG A:156	BINDING SITE FOR RESIDUE SO4 A 203
2	AC2	SOFTWARE	GLU A:94 , GLY A:118 , LYS A:151 , ARG A:152	BINDING SITE FOR RESIDUE SO4 A 204
3	AC3	SOFTWARE	CYS B:150 , LYS B:151 , ARG B:152 , GLY B:153 , LYS B:154 , HIS B:155 , ARG B:156	BINDING SITE FOR RESIDUE SO4 B 203
4	AC4	SOFTWARE	GLY B:118 , LYS B:151 , ARG B:152 , ARG B:156	BINDING SITE FOR RESIDUE SO4 B 204

(no "SS Bond" information available for 2Q47)

Asymmetric Unit

No.	Model	Residues
1	1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16	His A:144	-	Pro A:145
2	1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16	His B:144	-	Pro B:145

(no "SAP(SNP)/Variant" information available for 2Q47)

Asymmetric Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	TYR_PHOSPHATASE_1	PS00383	Tyrosine specific protein phosphatases active site.	Y1500_ARATH	148-158	2	A:148-158 B:148-158

Biological Unit 1 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	TYR_PHOSPHATASE_1	PS00383	Tyrosine specific protein phosphatases active site.	Y1500_ARATH	148-158	2	A:148-158 B:148-158

Biological Unit 2 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	TYR_PHOSPHATASE_1	PS00383	Tyrosine specific protein phosphatases active site.	Y1500_ARATH	148-158	2	A:148-158 B:148-158

(no "Exon" information available for 2Q47)

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
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Chain A from PDB  Type:PROTEIN  Length:151
 aligned with Y1500_ARATH | Q9ZVN4 from UniProtKB/Swiss-Prot  Length:215

    Alignment length:151
                                    61        71        81        91       101       111       121       131       141       151       161       171       181       191       201 
          Y1500_ARATH    52 HLIPPLNFSMVDNGIFRSGFPDSANFSFLQTLGLRSIIYLCPEPYPESNLQFLKSNGIRLFQFGIEGNKEPFVNIPDHKIRMALKVLLDEKNHPVLIHCKRGKHRTGCLVGCLRKLQKWCLTSIFDEYQRFAAAKARVSDQRFMEIFDVSS 202
               SCOP domains d2q47a1 A:52-202 Putative phosphatase At1g05000                                                                                                         SCOP domains
               CATH domains 2q47A00 A:52-202 Protein tyrosine phosphatase superfamily                                                                                               CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........ee....eeee...hhhhhhhhh.....eeee......hhhhhhhhhh...eee..............hhhhhhhhhhhhhhhhhh.eeee.....hhhhhhhhhhhhhh..hhhhhhhhhhhhhh....hhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------TYR_PHOSPHA-------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2q47 A  52 HLIPPLNFSmVDNGIFRSGFPDSANFSFLQTLGLRSIIYLCPEPYPESNLQFLKSNGIRLFQFGIEGNKEPFVNIPDHKIRmALKVLLDEKNHPVLIHCKRGKHRTGCLVGCLRKLQKWCLTSIFDEYQRFAAAKARVSDQRFmEIFDVSS 202
                                    61        71        81        91       101       111       121       131 |     141       151       161       171       181       191   |   201 
                                    61-MSE                                                                 133-MSE                                                       195-MSE

Chain B from PDB  Type:PROTEIN  Length:151
 aligned with Y1500_ARATH | Q9ZVN4 from UniProtKB/Swiss-Prot  Length:215

    Alignment length:151
                                    61        71        81        91       101       111       121       131       141       151       161       171       181       191       201 
          Y1500_ARATH    52 HLIPPLNFSMVDNGIFRSGFPDSANFSFLQTLGLRSIIYLCPEPYPESNLQFLKSNGIRLFQFGIEGNKEPFVNIPDHKIRMALKVLLDEKNHPVLIHCKRGKHRTGCLVGCLRKLQKWCLTSIFDEYQRFAAAKARVSDQRFMEIFDVSS 202
               SCOP domains d2q47b1 B:52-202 Putative phosphatase At1g05000                                                                                                         SCOP domains
               CATH domains 2q47B00 B:52-202 Protein tyrosine phosphatase superfamily                                                                                               CATH domains
           Pfam domains (1) -Y_phosphatase2-2q47B01 B:53-202                                                                                                                        Pfam domains (1)
           Pfam domains (2) -Y_phosphatase2-2q47B02 B:53-202                                                                                                                        Pfam domains (2)
         Sec.struct. author ........eeee..eee.......hhhhhhhhh..eeee......hhhhhhhhhhh..eeee......hhhhh..hhhhhhhhhhhhhh..............hhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------TYR_PHOSPHA-------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2q47 B  52 HLIPPLNFSmVDNGIFRSGFPDSANFSFLQTLGLRSIIYLCPEPYPESNLQFLKSNGIRLFQFGIEGNKEPFVNIPDHKIRmALKVLLDEKNHPVLIHCKRGKHRTGCLVGCLRKLQKWCLTSIFDEYQRFAAAKARVSDQRFmEIFDVSS 202
                                    61        71        81        91       101       111       121       131 |     141       151       161       171       181       191   |   201 
                                    61-MSE                                                                 133-MSE                                                       195-MSE

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(

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Folds(

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Superfamilies( (-)

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Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: Alpha and beta proteins (a/b) (23833)

Fold: (Phosphotyrosine protein) phosphatases II (296)

Superfamily: (Phosphotyrosine protein) phosphatases II (296)

Family: Dual specificity phosphatase-like (27)

Protein domain: Putative phosphatase At1g05000 (2)

Thale cress (Arabidopsis thaliana) [TaxId: 3702] (2)

1a	d2q47a1	A:52-202
1b	d2q47b1	B:52-202

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: Alpha-Beta Complex (3881)

Topology: Protein-Tyrosine Phosphatase; Chain A (262)

Homologous Superfamily: Protein tyrosine phosphatase superfamily (228)

Thale cress (Arabidopsis thaliana) (2)

1a	2q47A00	A:52-202
1b	2q47B00	B:52-202

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: Phosphatase (121)

Family: Y_phosphatase2 (1)

Arabidopsis thaliana (Mouse-ear cress) (1)

1a	Y_phosphatase2-2q47B01	B:53-202
1b	Y_phosphatase2-2q47B02	B:53-202

Asymmetric Unit(hide GO term definitions)

Chain A,B (Y1500_ARATH | Q9ZVN4)

molecular function
	GO:0016787	hydrolase activity	Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
	GO:0016791	phosphatase activity	Catalysis of the hydrolysis of phosphoric monoesters, releasing inorganic phosphate.
	GO:0004721	phosphoprotein phosphatase activity	Catalysis of the reaction: a phosphoprotein + H2O = a protein + phosphate. Together with protein kinases, these enzymes control the state of phosphorylation of cell proteins and thereby provide an important mechanism for regulating cellular activity.
	GO:0004725	protein tyrosine phosphatase activity	Catalysis of the reaction: protein tyrosine phosphate + H2O = protein tyrosine + phosphate.
biological process
	GO:0016311	dephosphorylation	The process of removing one or more phosphoric (ester or anhydride) residues from a molecule.
	GO:0035335	peptidyl-tyrosine dephosphorylation	The removal of phosphoric residues from peptidyl-O-phospho-tyrosine to form peptidyl-tyrosine.
	GO:0006470	protein dephosphorylation	The process of removing one or more phosphoric residues from a protein.

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	Y1500_ARATH \| Q9ZVN4	:	1xri

1xri	ORIGINAL REFINEMENT BASED ON SAME DATA AND R-FREE SET.

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