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Title :   CRYSTAL STRUCTURE OF THE PUTATIVE PYROPHOSPHATASE YPJD FROM BACILLUS SUBTILIS. NORTHEAST STRUCTURAL GENOMICS CONSORTIUM TARGET SR428.

Authors :   S. M. Vorobiev, W. Zhou, J. Seetharaman, D. Wang, L. C. Ma, T. Acton, R. Xio, G. T. Montelione, L. Tong, J. F. Hunt, Northeast Structural Genomics Consortium (Nesg)

Date :   27 Apr 06 (Deposition) - 23 May 06 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.90

Chains :   Asym./Biol. Unit : A,B,C,D

Keywords :   Pyrophosphatase, Ypjd, Nesg, Structural Genomics, Psi, Protein Structure Initiative, Northeast Structural Genomics Consortium, Unknown Function (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. M. Vorobiev, W. Zhou, J. Seetharaman, D. Wang, L. C. Ma, T. Acton, R. Xio, G. T. Montelione, L. Tong, J. F. Hunt
Crystal Structure Of The Putative Pyrophosphatase Ypjd From Bacillus Subtilis.
To Be Published
PubMed: search
(for further references see the PDB file header)

Molecule 1 - HYPOTHETICAL PROTEIN YPJD
	Chains	:	A, B, C, D
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Strain	:	BL21(DE3)+MAGIC
	Expression System Taxid	:	562
	Expression System Vector Type	:	PET21
	Gene	:	YPJD
	Organism Scientific	:	BACILLUS SUBTILIS
	Organism Taxid	:	1423
	Strain	:	168

		1	2	3	4
Asymmetric/Biological Unit	:	A	B	C	D

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (2, 26)

No.	Name	Count	Type	Full Name
1	MSE	22	Mod. Amino Acid	SELENOMETHIONINE
2	NA	4	Ligand/Ion	SODIUM ION

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLU D:37 , GLU D:40 , GLU D:66 , ASP D:69	BINDING SITE FOR RESIDUE NA D 301
2	AC2	SOFTWARE	GLU B:37 , GLU B:40 , GLU B:66 , ASP B:69	BINDING SITE FOR RESIDUE NA B 302
3	AC3	SOFTWARE	GLU C:37 , GLU C:40 , GLU C:66 , ASP C:69	BINDING SITE FOR RESIDUE NA C 303
4	AC4	SOFTWARE	GLU A:37 , GLU A:40 , GLU A:66 , ASP A:69 , HOH A:463	BINDING SITE FOR RESIDUE NA A 304

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

(no "Cis Peptide Bond" information available for 2GTA)

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

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

(no "Exon" information available for 2GTA)

Asymmetric/Biological 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:98
 aligned with YPJD_BACSU | P42979 from UniProtKB/Swiss-Prot  Length:111

    Alignment length:98
                                    10        20        30        40        50        60        70        80        90        
           YPJD_BACSU     1 MSDKTMKDIQAEVDRYIGQFKEGYFSPLAMMARLTEELGELAREVNHRYGEKPKKATEDDKSMEEEIGDVLFVLVCLANSLDISLEEAHDRVMHKFNT  98
               SCOP domains d2gtaa1 A:1-98 Hypothetical protein YpjD                                                           SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhh...........hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------- Transcript
                 2gta A   1 mSDKTmKDIQAEVDRYIGQFKEGYFSPLAmmARLTEELGELAREVNHRYGEKPKKATEDDKSmEEEIGDVLFVLVCLANSLDISLEEAHDRVmHKFNT  98
                            |    |  10        20        30|       40        50        60  |     70        80        90  |     
                            |    |                      30-MSE                           63-MSE                        93-MSE 
                            1-MSE|                       31-MSE                                                               
                                 6-MSE

Chain B from PDB  Type:PROTEIN  Length:96
 aligned with YPJD_BACSU | P42979 from UniProtKB/Swiss-Prot  Length:111

    Alignment length:100
                                    10        20        30        40        50        60        70        80        90       100
           YPJD_BACSU     1 MSDKTMKDIQAEVDRYIGQFKEGYFSPLAMMARLTEELGELAREVNHRYGEKPKKATEDDKSMEEEIGDVLFVLVCLANSLDISLEEAHDRVMHKFNTRD 100
               SCOP domains d2gtab1 B:1-100 Hypothetical protein YpjD                                                            SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhh.......----.hhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------- Transcript
                 2gta B   1 mSDKTmKDIQAEVDRYIGQFKEGYFSPLAmmARLTEELGELAREVNHRYGEKPKKA----KSmEEEIGDVLFVLVCLANSLDISLEEAHDRVmHKFNTRD 100
                            |    |  10        20        30|       40        50     |   -| |     70        80        90  |    100
                            1-MSE|                      30-MSE                    56   61 |                            93-MSE   
                                 6-MSE                   31-MSE                          63-MSE

Chain C from PDB  Type:PROTEIN  Length:86
 aligned with YPJD_BACSU | P42979 from UniProtKB/Swiss-Prot  Length:111

    Alignment length:98
                                    11        21        31        41        51        61        71        81        91        
           YPJD_BACSU     2 SDKTMKDIQAEVDRYIGQFKEGYFSPLAMMARLTEELGELAREVNHRYGEKPKKATEDDKSMEEEIGDVLFVLVCLANSLDISLEEAHDRVMHKFNTR  99
               SCOP domains d2gtac1 C:2-99 Hypothetical protein YpjD                                                           SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhh------------hhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------- Transcript
                 2gta C   2 SDKTmKDIQAEVDRYIGQFKEGYFSPLAmmARLTEELGELAREVNHRY------------SmEEEIGDVLFVLVCLANSLDISLEEAHDRVmHKFNTR  99
                                |   11        21        31        41       | -         -||      71        81        91 |      
                                6-MSE                  30-MSE             49           62|                            93-MSE  
                                                        31-MSE                          63-MSE

Chain D from PDB  Type:PROTEIN  Length:97
 aligned with YPJD_BACSU | P42979 from UniProtKB/Swiss-Prot  Length:111

    Alignment length:113
                                                                                                                                       111   
                                    11        21        31        41        51        61        71        81        91       101       111   
           YPJD_BACSU     2 SDKTMKDIQAEVDRYIGQFKEGYFSPLAMMARLTEELGELAREVNHRYGEKPKKATEDDKSMEEEIGDVLFVLVCLANSLDISLEEAHDRVMHKFNTRDKDRWTRKEEGK---   -
               SCOP domains d2gtad1 D:2-111 Hypothetical protein YpjD                                                                     --- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhh.---------hhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh-------...hhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------- Transcript
                 2gta D   2 SDKTmKDIQAEVDRYIGQFKEGYFSPLAmmARLTEELGELAREVNHRYGE---------KSmEEEIGDVLFVLVCLANSLDISLEEAHDRVmHKFNT-------RKEEGKLEH 114
                                |   11        21        31        41        51        61 |      71        81        91 |    |  -    |  111   
                                6-MSE                  30-MSE               51        61 |                            93-MSE8     106        
                                                        31-MSE                          63-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/Biological Unit

Classes(

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Folds(

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Families(

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Protein Domains( (-)

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Class: All alpha proteins (14657)

Fold: all-alpha NTP pyrophosphatases (26)

Superfamily: all-alpha NTP pyrophosphatases (26)

Family: MazG-like (6)

Protein domain: Hypothetical protein YpjD (1)

Bacillus subtilis [TaxId: 1423] (1)

1a	d2gtaa1	A:1-98
1b	d2gtab1	B:1-100
1c	d2gtac1	C:2-99
1d	d2gtad1	D:2-111

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

(no "Pfam Domain" information available for 2GTA)

Asymmetric/Biological Unit(hide GO term definitions)

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

Asymmetric/Biological Unit
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Description

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Ligands, Modified Residues, Ions (2, 26)

Sites (4, 4)

SS Bonds (0, 0)

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