3D63 - JenaLib

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Title :   CRYSTAL STRUCTURE OF INORGANIC PYROPHOSPHATASE FROM BURKHOLDERIA PSEUDOMALLEI

Authors :   Seattle Structural Genomics Center For Infectious Disease (S

Date :   18 May 08 (Deposition) - 08 Jul 08 (Release) - 30 Oct 13 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.30

Chains :   Asym. Unit : A,B,C
Biol. Unit 1: A (1x),B (1x),C (1x)
Biol. Unit 2: A  (1x)
Biol. Unit 3: B  (1x)
Biol. Unit 4: C  (1x)

Keywords :   Structural Genomics, Ssgcid, Pyrophosphatase, Hydrolase, Seattle Structural Genomics Center For Infectious Disease (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   L. Baugh, L. A. Gallagher, R. Patrapuvich, M. C. Clifton, A. S. Gardberg, T. E. Edwards, B. Armour, D. W. Begley, S. H. Dieterich, D. M. Dranow, J. Abendroth, J. W. Fairman, D. Fox, B. L. Staker, I. Phan, A. Gillespie, R. Choi, S. Nakazawa-Hewitt, M. T. Nguyen, A. Napuli, L. Barrett, G. W. Buchko, R. Stacy, P. J. Myler, L. J. Stewart, C. Manoil W. C. Van Voorhis
Combining Functional And Structural Genomics To Sample The Essential Burkholderia Structome.
Plos One V. 8 53851 2013
PubMed-ID: 23382856 | Reference-DOI: 10.1371/JOURNAL.PONE.0053851

Molecule 1 - INORGANIC PYROPHOSPHATASE
	Chains	:	A, B, C
	EC Number	:	3.6.1.1
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	AVA0421
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	PPA, BURPS1710B_1237
	Organism Scientific	:	BURKHOLDERIA PSEUDOMALLEI
	Organism Taxid	:	320372
	Strain	:	1710B

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

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 3D63)

(no "Site" information available for 3D63)

(no "SS Bond" information available for 3D63)

Asymmetric Unit

No.	Residues
1	Leu A:12	-	Pro A:13
2	Leu B:12	-	Pro B:13
3	Leu C:12	-	Pro C:13

(no "SAP(SNP)/Variant" information available for 3D63)

(no "PROSITE Motif" information available for 3D63)

(no "Exon" information available for 3D63)

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:173
 aligned with Q3JUV5_BURP1 | Q3JUV5 from UniProtKB/TrEMBL  Length:175

    Alignment length:173
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172   
         Q3JUV5_BURP1     3 FSNVPAGKDLPQDFNVIIEIPAQSEPVKYEADKALGLLVVDRFIGTGMRYPVNYGFIPQTLSGDGDPVDVLVITPFPLLAGSVVRARALGMLKMTDESGVDAKLVAVPHDKVCPMTANLKSIDDVPAYLKDQIKHFFEQYKALEKGKWVKVEGWDGIDAAHKEITDGVANFKK 175
               SCOP domains d3d63a_ A: automated matches                                                                                                                                                  SCOP domains
               CATH domains 3d63A00 A:3-175 Inorganic Pyrophosphatase                                                                                                                                     CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .............eeeeeee......eeeeee....eeeeeee.........eeee............eeee..........eeeeeeeeeeeeee..eeeeeeeeee............hhhhhhhhhhhhhhhhhhhhh.......eeeeeeehhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3d63 A   3 FSNVPAGKDLPQDFNVIIEIPAQSEPVKYEADKALGLLVVDRFIGTGMRYPVNYGFIPQTLSGDGDPVDVLVITPFPLLAGSVVRARALGMLKMTDESGVDAKLVAVPHDKVCPMTANLKSIDDVPAYLKDQIKHFFEQYKALEKGKWVKVEGWDGIDAAHKEITDGVANFKK 175
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172

Chain B from PDB  Type:PROTEIN  Length:173
 aligned with Q3JUV5_BURP1 | Q3JUV5 from UniProtKB/TrEMBL  Length:175

    Alignment length:173
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172   
         Q3JUV5_BURP1     3 FSNVPAGKDLPQDFNVIIEIPAQSEPVKYEADKALGLLVVDRFIGTGMRYPVNYGFIPQTLSGDGDPVDVLVITPFPLLAGSVVRARALGMLKMTDESGVDAKLVAVPHDKVCPMTANLKSIDDVPAYLKDQIKHFFEQYKALEKGKWVKVEGWDGIDAAHKEITDGVANFKK 175
               SCOP domains d3d63b_ B: automated matches                                                                                                                                                  SCOP domains
               CATH domains 3d63B00 B:3-175 Inorganic Pyrophosphatase                                                                                                                                     CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .............eeeeeee......eeeeee....eeeeeee.........eeee............eeee..........eeeeeeeeeeeeee..eeeeeeeeee....hhhhh...hhhhhhhhhhhhhhhhhhhhh.......eeeeeeehhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3d63 B   3 FSNVPAGKDLPQDFNVIIEIPAQSEPVKYEADKALGLLVVDRFIGTGMRYPVNYGFIPQTLSGDGDPVDVLVITPFPLLAGSVVRARALGMLKMTDESGVDAKLVAVPHDKVCPMTANLKSIDDVPAYLKDQIKHFFEQYKALEKGKWVKVEGWDGIDAAHKEITDGVANFKK 175
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172

Chain C from PDB  Type:PROTEIN  Length:178
 aligned with Q3JUV5_BURP1 | Q3JUV5 from UniProtKB/TrEMBL  Length:175

    Alignment length:178
                               1                                                                                                                                                                              
                               |     7        17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167        
         Q3JUV5_BURP1     - ---MSFSNVPAGKDLPQDFNVIIEIPAQSEPVKYEADKALGLLVVDRFIGTGMRYPVNYGFIPQTLSGDGDPVDVLVITPFPLLAGSVVRARALGMLKMTDESGVDAKLVAVPHDKVCPMTANLKSIDDVPAYLKDQIKHFFEQYKALEKGKWVKVEGWDGIDAAHKEITDGVANFKK 175
               SCOP domains ------d3d63c1 C:4-175 automated matches                                                                                                                                            SCOP domains
               CATH domains 3d63C00 C:-19-175 Inorganic Pyrophosphatase                                                                                                                                        CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..................eeeeeee......eeeeee....eeeeeee.........eeeee..........eeeee..........eeeeeeeeeeeeee..eeeeeeeeee....hhhhh........hhhhhhhhhhhhhhh........eeeeeeehhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3d63 C -19 AHHHHHSNVPAGKDLPQDFNVIIEIPAQSEPVKYEADKALGLLVVDRFIGTGMRYPVNYGFIPQTLSGDGDPVDVLVITPFPLLAGSVVRARALGMLKMTDESGVDAKLVAVPHDKVCPMTANLKSIDDVPAYLKDQIKHFFEQYKALEKGKWVKVEGWDGIDAAHKEITDGVANFKK 175
                                 ||  7        17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167        
                               -14|                                                                                                                                                                           
                                  4

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( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: All beta proteins (24004)

Fold: OB-fold (1179)

Superfamily: Inorganic pyrophosphatase (69)

Family: Inorganic pyrophosphatase (56)

Protein domain: automated matches (15)

Burkholderia pseudomallei [TaxId: 320372] (6)

1a	d3d63a_	A:
1b	d3d63b_	B:
1c	d3d63c1	C:4-175

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

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Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: Alpha-Beta Complex (3881)

Topology: Inorganic Pyrophosphatase (59)

Homologous Superfamily: Inorganic Pyrophosphatase (59)

Burkholderia pseudomallei 1710b. Organism_taxid: 320372. Strain: 1710b. (2)

1a	3d63C00	C:-19-175
1b	3d63A00	A:3-175
1c	3d63B00	B:3-175

(no "Pfam Domain" information available for 3D63)

Asymmetric Unit(hide GO term definitions)

Chain A,B,C (Q3JUV5_BURP1 | Q3JUV5)

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:0004427	inorganic diphosphatase activity	Catalysis of the reaction: diphosphate + H(2)O = H(+) + 2 phosphate.
	GO:0000287	magnesium ion binding	Interacting selectively and non-covalently with magnesium (Mg) ions.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
biological process
	GO:0006796	phosphate-containing compound metabolic process	The chemical reactions and pathways involving the phosphate group, the anion or salt of any phosphoric acid.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

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	Cis Peptide Bonds
		Leu A:12 - Pro A:13	[ RasMol ]
		Leu B:12 - Pro B:13	[ RasMol ]
		Leu C:12 - Pro C:13	[ RasMol ]

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	Q3JUV5_BURP1 \| Q3JUV5	:	3eiy 3eiz 3ej0 3ej2 3gvf

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