3KB2 - JenaLib

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Title :   CRYSTAL STRUCTURE OF YORR PROTEIN IN COMPLEX WITH PHOSPHORYLATED GDP FROM BACILLUS SUBTILIS, NORTHEAST STRUCTURAL GENOMICS CONSORTIUM TARGET SR256

Authors :   F. Forouhar, D. Friedman, J. Seetharaman, J. Janjua, R. Xiao, K. Cunningham, L. Ma, C. Ho, J. K. Everett, R. Nair, T. B. Acton, B. Rost, G. T. Montelione, L. Tong, J. F. Hunt, Northeast Structural Genomics Consortium (Nesg)

Date :   20 Oct 09 (Deposition) - 27 Oct 09 (Release) - 27 Oct 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.20

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

Keywords :   Alpha-Beta Protein. , Structural Genomics, Psi-2, Protein Structure Initiative, Northeast Structural Genomics Consortium, Nesg (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   F. Forouhar, D. Friedman, J. Seetharaman, J. Janjua, R. Xiao, K. Cunningham, L. Ma, C. Ho, J. K. Everett, R. Nair, T. B. Acton, B. Rost, G. T. Montelione, L. Tong, J. F. Hunt
Northeast Structural Genomics Consortium Target Sr256
To Be Published
PubMed: search
(for further references see the PDB file header)

Molecule 1 - SPBC2 PROPHAGE-DERIVED UNCHARACTERIZED PROTEIN YORR
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	PET21
	Expression System Strain	:	BL21(DE3)+ MAGIC
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Gene	:	BSU20280, YORR
	Organism Scientific	:	BACILLUS SUBTILIS
	Organism Taxid	:	1423
	Strain	:	168

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 6)

No.	Name	Count	Type	Full Name
1	G3D	2	Ligand/Ion	GUANOSINE-3'-MONOPHOSPHATE-5'-DIPHOSPHATE
2	MG	2	Ligand/Ion	MAGNESIUM ION
3	MSE	2	Mod. Amino Acid	SELENOMETHIONINE

Biological Unit 1 (2, 4)

No.	Name	Count	Type	Full Name
1	G3D	2	Ligand/Ion	GUANOSINE-3'-MONOPHOSPHATE-5'-DIPHOSPHATE
2	MG	-1	Ligand/Ion	MAGNESIUM ION
3	MSE	2	Mod. Amino Acid	SELENOMETHIONINE

Biological Unit 2 (2, 2)

No.	Name	Count	Type	Full Name
1	G3D	1	Ligand/Ion	GUANOSINE-3'-MONOPHOSPHATE-5'-DIPHOSPHATE
2	MG	-1	Ligand/Ion	MAGNESIUM ION
3	MSE	1	Mod. Amino Acid	SELENOMETHIONINE

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	CYS A:11 , CYS A:12 , PHE A:13 , LYS A:14 , SER A:15 , THR A:16 , SER A:152 , SER A:153 , MG A:181 , HOH A:227 , HOH A:234 , HOH A:268 , HOH A:269	BINDING SITE FOR RESIDUE G3D A 180
2	AC2	SOFTWARE	SER A:15 , G3D A:180 , HOH A:268 , HOH A:269 , HOH A:270 , HOH B:231	BINDING SITE FOR RESIDUE MG A 181
3	AC3	SOFTWARE	ASP B:10 , CYS B:11 , CYS B:12 , PHE B:13 , LYS B:14 , SER B:15 , THR B:16 , SER B:152 , SER B:153 , HOH B:175 , HOH B:176 , MG B:181 , HOH B:217 , HOH B:230 , HOH B:235	BINDING SITE FOR RESIDUE G3D B 180
4	AC4	SOFTWARE	SER B:15 , ASP B:61 , HOH B:175 , HOH B:176 , G3D B:180	BINDING SITE FOR RESIDUE MG B 181

(no "SS Bond" information available for 3KB2)

(no "Cis Peptide Bond" information available for 3KB2)

(no "SAP(SNP)/Variant" information available for 3KB2)

(no "PROSITE Motif" information available for 3KB2)

(no "Exon" information available for 3KB2)

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:171
 aligned with YORR_BACSU | O31896 from UniProtKB/Swiss-Prot  Length:165

    Alignment length:171
                                                                                                                                                                                             165       
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161   |     - 
           YORR_BACSU     2 TLIILEGPDCCFKSTVAAKLSKELKYPIIKGSSFELAKSGNEKLFEHFNKLADEDNVIIDRFVYSNLVYAKKFKDYSILTERQLRFIEDKIKAKAKVVYLHADPSVIKKRLRVRGDEYIEGKDIDSILELYREVMSNAGLHTYSWDTGQWSSDEIAKDIIFLVE-------   -
               SCOP domains d3kb2a_ A: automated matches                                                                                                                                                SCOP domains
               CATH domains 3kb2A00 A:2-172 P-loop containing nucleotide triphosphate hydrolases                                                                                                        CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee.....hhhhhhhhhhhhhh..eee..hhhhhh.hhhhhhhhhhhhh....eeee.hhhhhhhhh.........hhhhhhhhhhhhh..eeeeeee.hhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhh....eeeee....hhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3kb2 A   2 TLIILEGPDCCFKSTVAAKLSKELKYPIIKGSSFELAKSGNEKLFEHFNKLADEDNVIIDRFVYSNLVYAKKFKDYSILTERQLRFIEDKIKAKAKVVYLHADPSVIKKRLRVRGDEYIEGKDIDSILELYREVmSNAGLHTYSWDTGQWSSDEIAKDIIFLVELEHHHHH 172
                                    11        21        31        41        51        61        71        81        91       101       111       121       131    |  141       151       161       171 
                                                                                                                                                                136-MSE

Chain B from PDB  Type:PROTEIN  Length:167
 aligned with YORR_BACSU | O31896 from UniProtKB/Swiss-Prot  Length:165

    Alignment length:171
                                                                                                                                                                                             165       
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161   |     - 
           YORR_BACSU     2 TLIILEGPDCCFKSTVAAKLSKELKYPIIKGSSFELAKSGNEKLFEHFNKLADEDNVIIDRFVYSNLVYAKKFKDYSILTERQLRFIEDKIKAKAKVVYLHADPSVIKKRLRVRGDEYIEGKDIDSILELYREVMSNAGLHTYSWDTGQWSSDEIAKDIIFLVE-------   -
               SCOP domains d3kb2b_ B: automated matches                                                                                                                                                SCOP domains
               CATH domains 3kb2B00 B:2-172 P-loop containing nucleotide triphosphate hydrolases                                                                                                        CATH domains
           Pfam domains (1) --AAA_18-3kb2B01 B:4-130                                                                                                         ------------------------------------------ Pfam domains (1)
           Pfam domains (2) --AAA_18-3kb2B02 B:4-130                                                                                                         ------------------------------------------ Pfam domains (2)
         Sec.struct. author .eeeee.....hhhhhhhhhhhhhh..eee..hhhhhhhhhhhhhhhhhhhhh...eeee.hhhhhhhhh.........hhhhhhhhhhhhh..eeeeeee.hhhhhhhhh.......----hhhhhhhhhhhhhhh....eeeee....hhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3kb2 B   2 TLIILEGPDCCFKSTVAAKLSKELKYPIIKGSSFELAKSGNEKLFEHFNKLADEDNVIIDRFVYSNLVYAKKFKDYSILTERQLRFIEDKIKAKAKVVYLHADPSVIKKRLRVRGDEY----DIDSILELYREVmSNAGLHTYSWDTGQWSSDEIAKDIIFLVELEHHHHH 172
                                    11        21        31        41        51        61        71        81        91       101       111       | -  |    131    |  141       151       161       171 
                                                                                                                                               119  124         136-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(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

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

Fold: P-loop containing nucleoside triphosphate hydrolases (2083)

Superfamily: P-loop containing nucleoside triphosphate hydrolases (2083)

Family: Nucleotide and nucleoside kinases (231)

Protein domain: automated matches (25)

Bacillus subtilis [TaxId: 1423] (1)

1a	d3kb2a_	A:
1b	d3kb2b_	B:

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

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Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 3-Layer(aba) Sandwich (12045)

Topology: Rossmann fold (7312)

Homologous Superfamily: P-loop containing nucleotide triphosphate hydrolases (1378)

Bacillus subtilis. Organism_taxid: 1423. Strain: 168. (6)

1a	3kb2A00	A:2-172
1b	3kb2B00	B:2-172

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: P-loop_NTPase (1112)

Family: AAA_18 (7)

Bacillus subtilis (1)

1a	AAA_18-3kb2B01	B:4-130
1b	AAA_18-3kb2B02	B:4-130

Asymmetric Unit(hide GO term definitions)

(no "Gene Ontology" information available for 3KB2)

Asymmetric Unit
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	YORR_BACSU \| O31896	:	2axp

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Description

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Ligands, Modified Residues, Ions (3, 6)

Sites (4, 4)

SS Bonds (0, 0)

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