2NWA - JenaLib

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Title :   X-RAY CRYSTAL STRUCTURE OF PROTEIN YTMB FROM BACILLUS SUBTILIS. NORTHEAST STRUCTURAL GENOMICS CONSORTIUM TARGET SR466

Authors :   W. Zhou, F. Forouhar, J. Seetharaman, D. Wang, K. Cunningham, L. -C. Ma, Y. Fang, R. Xiao, M. C. Baran, T. B. Acton, G. T. Montelione, J. F. Hunt, L. Tong, Northeast Structural Genomics Consortium (Nesg)

Date :   14 Nov 06 (Deposition) - 09 Jan 07 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.70

Chains :   Asym. Unit : A,B,C,D,E,F,G,H
Biol. Unit 1: A,B,C,D  (1x)
Biol. Unit 2: E,F,G,H  (1x)
Biol. Unit 3: A (1x),B (1x),C (1x),D (1x),E (1x),F (1x),G (1x),H (1x)

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

Reference :   W. Zhou, F. Forouhar, J. Seetharaman, D. Wang, K. Cunningham, L. -C. Ma, Y. Fang, R. Xiao, M. C. Baran, T. B. Acton, G. T. Montelione, J. F. Hunt, L. Tong
Crystal Structure Of The Hypothetical Protein Ytmb From Bacillus Subtilis Subsp. (Subtilis Str. 168), Northeast Structural Genomics Target Sr466
To Be Published
PubMed: search
(for further references see the PDB file header)

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

		1	2	3	4	5	6	7	8
Asymmetric Unit	:	A	B	C	D	E	F	G	H
Biological Unit 1 (1x)	:	A	B	C	D
Biological Unit 2 (1x)	:					E	F	G	H
Biological Unit 3 (1x)	:	A (1x)	B (1x)	C (1x)	D (1x)	E (1x)	F (1x)	G (1x)	H (1x)

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 40)

No.	Name	Count	Type	Full Name
1	MSE	32	Mod. Amino Acid	SELENOMETHIONINE
2	SO4	8	Ligand/Ion	SULFATE ION

Biological Unit 1 (2, 20)

No.	Name	Count	Type	Full Name
1	MSE	16	Mod. Amino Acid	SELENOMETHIONINE
2	SO4	4	Ligand/Ion	SULFATE ION

Biological Unit 2 (2, 20)

No.	Name	Count	Type	Full Name
1	MSE	16	Mod. Amino Acid	SELENOMETHIONINE
2	SO4	4	Ligand/Ion	SULFATE ION

Biological Unit 3 (2, 20)

No.	Name	Count	Type	Full Name
1	MSE	16	Mod. Amino Acid	SELENOMETHIONINE
2	SO4	4	Ligand/Ion	SULFATE ION

Asymmetric Unit (8, 8)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLU A:6 , ARG A:33 , LYS A:47	BINDING SITE FOR RESIDUE SO4 A 201
2	AC2	SOFTWARE	LYS B:14 , LYS B:29 , ARG B:33 , HOH B:225	BINDING SITE FOR RESIDUE SO4 B 201
3	AC3	SOFTWARE	LYS C:14 , LYS C:29 , ARG C:33	BINDING SITE FOR RESIDUE SO4 C 201
4	AC4	SOFTWARE	LYS D:14 , LYS D:29 , ARG D:33 , LYS D:47	BINDING SITE FOR RESIDUE SO4 D 201
5	AC5	SOFTWARE	LYS E:29 , ARG E:33	BINDING SITE FOR RESIDUE SO4 E 201
6	AC6	SOFTWARE	GLU F:6 , ARG F:33 , LYS F:47	BINDING SITE FOR RESIDUE SO4 F 201
7	AC7	SOFTWARE	LYS G:14 , LYS G:29 , ARG G:33	BINDING SITE FOR RESIDUE SO4 G 201
8	AC8	SOFTWARE	LYS H:14 , LYS H:29 , ARG H:33 , LYS H:47	BINDING SITE FOR RESIDUE SO4 H 201

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

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

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

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

(no "Exon" information available for 2NWA)

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:80
 aligned with YTMB_BACSU | O34365 from UniProtKB/Swiss-Prot  Length:80

    Alignment length:81
                                                                                                          80 
                                    10        20        30        40        50        60        70        80 
            YTMB_BACSU    1 MGMPVEFNTLIVTKGKEVRIDENIFTLEKDGYRVYPMEIPMDVRKTKFGEKSGTAEVQKLQWEEGRTIITYKLTSLHSVN-  -
               SCOP domains d2nwaa1 A:1-80 Hypothetical protein YtmB                                        - SCOP domains
               CATH domains -2nwaA01 A:2-77 Hypothetical PUA domain-like; do main 1                      ---- CATH domains
               Pfam domains --------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee...ee.....ee....eeeeeee..ee.....eeeee....-...eeeeeeeeeee..eeeeeeeeeee..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------- Transcript
                  2nwa A  1 mGmPVEFNTLIVTKGKEVRIDENIFTLEKDGYRVYPmEIPmDVRKTKF-EKSGTAEVQKLQWEEGRTIITYKLTSLHSVNL 81
                            | |     10        20        30      | 40|      |50        60        70        80 
                            | |                                37-MSE     48 |                               
                            1-MSE                                  41-MSE   50                               
                              3-MSE

Chain B from PDB  Type:PROTEIN  Length:80
 aligned with YTMB_BACSU | O34365 from UniProtKB/Swiss-Prot  Length:80

    Alignment length:81
                                                                                                          80 
                                    10        20        30        40        50        60        70        80 
            YTMB_BACSU    1 MGMPVEFNTLIVTKGKEVRIDENIFTLEKDGYRVYPMEIPMDVRKTKFGEKSGTAEVQKLQWEEGRTIITYKLTSLHSVN-  -
               SCOP domains d2nwab_ B: Hypothetical protein YtmB                                              SCOP domains
               CATH domains -2nwaB01 B:2-77 Hypothetical PUA domain-like; do main 1                      ---- CATH domains
               Pfam domains --------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee...ee.....ee....eeeeeee..ee.....eeeee....-.eeeeeeeeeeeee..eeeeeeeeeee..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------- Transcript
                  2nwa B  1 mGmPVEFNTLIVTKGKEVRIDENIFTLEKDGYRVYPmEIPmDVRKTKF-EKSGTAEVQKLQWEEGRTIITYKLTSLHSVNL 81
                            | |     10        20        30      | 40|      |50        60        70        80 
                            1-MSE                              37-MSE     48 |                               
                              3-MSE                                41-MSE   50

Chain C from PDB  Type:PROTEIN  Length:80
 aligned with YTMB_BACSU | O34365 from UniProtKB/Swiss-Prot  Length:80

    Alignment length:81
                                                                                                          80 
                                    10        20        30        40        50        60        70        80 
            YTMB_BACSU    1 MGMPVEFNTLIVTKGKEVRIDENIFTLEKDGYRVYPMEIPMDVRKTKFGEKSGTAEVQKLQWEEGRTIITYKLTSLHSVN-  -
               SCOP domains d2nwac_ C: Hypothetical protein YtmB                                              SCOP domains
               CATH domains -2nwaC01 C:2-77 Hypothetical PUA domain-like; do main 1                      ---- CATH domains
               Pfam domains --------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee...ee.....ee....eeeeeee..ee.....eeeee....-...eeeeeeeeeee..eeeeeeeeeee..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------- Transcript
                  2nwa C  1 mGmPVEFNTLIVTKGKEVRIDENIFTLEKDGYRVYPmEIPmDVRKTKF-EKSGTAEVQKLQWEEGRTIITYKLTSLHSVNL 81
                            | |     10        20        30      | 40|      |50        60        70        80 
                            1-MSE                              37-MSE     48 |                               
                              3-MSE                                41-MSE   50

Chain D from PDB  Type:PROTEIN  Length:80
 aligned with YTMB_BACSU | O34365 from UniProtKB/Swiss-Prot  Length:80

    Alignment length:81
                                                                                                          80 
                                    10        20        30        40        50        60        70        80 
            YTMB_BACSU    1 MGMPVEFNTLIVTKGKEVRIDENIFTLEKDGYRVYPMEIPMDVRKTKFGEKSGTAEVQKLQWEEGRTIITYKLTSLHSVN-  -
               SCOP domains d2nwad_ D: Hypothetical protein YtmB                                              SCOP domains
               CATH domains -2nwaD01 D:2-77 Hypothetical PUA domain-like; do main 1                      ---- CATH domains
               Pfam domains --------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee...ee.....ee....eeeeeee..ee.....eeeee....-...eeeeeeeeeee..eeeeeeeeeee..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------- Transcript
                  2nwa D  1 mGmPVEFNTLIVTKGKEVRIDENIFTLEKDGYRVYPmEIPmDVRKTKF-EKSGTAEVQKLQWEEGRTIITYKLTSLHSVNL 81
                            | |     10        20        30      | 40|      |50        60        70        80 
                            1-MSE                              37-MSE     48 |                               
                              3-MSE                                41-MSE   50

Chain E from PDB  Type:PROTEIN  Length:80
 aligned with YTMB_BACSU | O34365 from UniProtKB/Swiss-Prot  Length:80

    Alignment length:81
                                                                                                          80 
                                    10        20        30        40        50        60        70        80 
            YTMB_BACSU    1 MGMPVEFNTLIVTKGKEVRIDENIFTLEKDGYRVYPMEIPMDVRKTKFGEKSGTAEVQKLQWEEGRTIITYKLTSLHSVN-  -
               SCOP domains d2nwae_ E: Hypothetical protein YtmB                                              SCOP domains
               CATH domains -2nwaE01 E:2-77 Hypothetical PUA domain-like; do main 1                      ---- CATH domains
               Pfam domains --------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee...ee.....ee....eeeeeee..ee.....eeeee....-...eeeeeeeeeee..eeeeeeeeeee..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------- Transcript
                  2nwa E  1 mGmPVEFNTLIVTKGKEVRIDENIFTLEKDGYRVYPmEIPmDVRKTKF-EKSGTAEVQKLQWEEGRTIITYKLTSLHSVNL 81
                            | |     10        20        30      | 40|      |50        60        70        80 
                            1-MSE                              37-MSE     48 |                               
                              3-MSE                                41-MSE   50

Chain F from PDB  Type:PROTEIN  Length:80
 aligned with YTMB_BACSU | O34365 from UniProtKB/Swiss-Prot  Length:80

    Alignment length:81
                                                                                                          80 
                                    10        20        30        40        50        60        70        80 
            YTMB_BACSU    1 MGMPVEFNTLIVTKGKEVRIDENIFTLEKDGYRVYPMEIPMDVRKTKFGEKSGTAEVQKLQWEEGRTIITYKLTSLHSVN-  -
               SCOP domains d2nwaf_ F: Hypothetical protein YtmB                                              SCOP domains
               CATH domains -2nwaF01 F:2-77 Hypothetical PUA domain-like; do main 1                      ---- CATH domains
               Pfam domains --------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee...ee.....ee....eeeeeee..ee.....eeeee....-...eeeeeeeeeee..eeeeeeeeeee..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------- Transcript
                  2nwa F  1 mGmPVEFNTLIVTKGKEVRIDENIFTLEKDGYRVYPmEIPmDVRKTKF-EKSGTAEVQKLQWEEGRTIITYKLTSLHSVNL 81
                            | |     10        20        30      | 40|      |50        60        70        80 
                            1-MSE                              37-MSE     48 |                               
                              3-MSE                                41-MSE   50

Chain G from PDB  Type:PROTEIN  Length:80
 aligned with YTMB_BACSU | O34365 from UniProtKB/Swiss-Prot  Length:80

    Alignment length:81
                                                                                                          80 
                                    10        20        30        40        50        60        70        80 
            YTMB_BACSU    1 MGMPVEFNTLIVTKGKEVRIDENIFTLEKDGYRVYPMEIPMDVRKTKFGEKSGTAEVQKLQWEEGRTIITYKLTSLHSVN-  -
               SCOP domains d2nwag_ G: Hypothetical protein YtmB                                              SCOP domains
               CATH domains -2nwaG01 G:2-77 Hypothetical PUA domain-like; do main 1                      ---- CATH domains
               Pfam domains --------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee...ee.....ee....eeeeeee..ee.....eeeee....-...eeeeeeeeeee..eeeeeeeeeee..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------- Transcript
                  2nwa G  1 mGmPVEFNTLIVTKGKEVRIDENIFTLEKDGYRVYPmEIPmDVRKTKF-EKSGTAEVQKLQWEEGRTIITYKLTSLHSVNL 81
                            | |     10        20        30      | 40|      |50        60        70        80 
                            1-MSE                              37-MSE     48 |                               
                              3-MSE                                41-MSE   50

Chain H from PDB  Type:PROTEIN  Length:80
 aligned with YTMB_BACSU | O34365 from UniProtKB/Swiss-Prot  Length:80

    Alignment length:81
                                                                                                          80 
                                    10        20        30        40        50        60        70        80 
            YTMB_BACSU    1 MGMPVEFNTLIVTKGKEVRIDENIFTLEKDGYRVYPMEIPMDVRKTKFGEKSGTAEVQKLQWEEGRTIITYKLTSLHSVN-  -
               SCOP domains d2nwah_ H: Hypothetical protein YtmB                                              SCOP domains
               CATH domains -2nwaH01 H:2-77 Hypothetical PUA domain-like; do main 1                      ---- CATH domains
           Pfam domains (1) DUF2584-2nwaH01 H:1-80                                                          - Pfam domains (1)
           Pfam domains (2) DUF2584-2nwaH02 H:1-80                                                          - Pfam domains (2)
           Pfam domains (3) DUF2584-2nwaH03 H:1-80                                                          - Pfam domains (3)
           Pfam domains (4) DUF2584-2nwaH04 H:1-80                                                          - Pfam domains (4)
           Pfam domains (5) DUF2584-2nwaH05 H:1-80                                                          - Pfam domains (5)
           Pfam domains (6) DUF2584-2nwaH06 H:1-80                                                          - Pfam domains (6)
           Pfam domains (7) DUF2584-2nwaH07 H:1-80                                                          - Pfam domains (7)
           Pfam domains (8) DUF2584-2nwaH08 H:1-80                                                          - Pfam domains (8)
         Sec.struct. author ..eeeee...ee.....ee....eeeeeee..ee.....eeeee....-.eeeeeeeeeeeee..eeeeeeeeeee..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------- Transcript
                  2nwa H  1 mGmPVEFNTLIVTKGKEVRIDENIFTLEKDGYRVYPmEIPmDVRKTKF-EKSGTAEVQKLQWEEGRTIITYKLTSLHSVNL 81
                            | |     10        20        30      | 40|      |50        60        70        80 
                            1-MSE                              37-MSE     48 |                               
                              3-MSE                                41-MSE   50

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: PUA domain-like (96)

Superfamily: PUA domain-like (96)

Family: YtmB-like (1)

Protein domain: Hypothetical protein YtmB (1)

Bacillus subtilis [TaxId: 1423] (1)

1a	d2nwaa1	A:1-80
1b	d2nwab_	B:
1c	d2nwac_	C:
1d	d2nwad_	D:
1e	d2nwae_	E:
1f	d2nwaf_	F:
1g	d2nwag_	G:
1h	d2nwah_	H:

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Beta (13760)

Architecture: Beta Barrel (4804)

Topology: Ribosomal Protein L25; Chain P (96)

Homologous Superfamily: Hypothetical PUA domain-like; domain 1 (7)

Bacillus subtilis. Organism_taxid: 1423. Strain: 168. (1)

1a	2nwaA01	A:2-77
1b	2nwaB01	B:2-77
1c	2nwaC01	C:2-77
1d	2nwaD01	D:2-77
1e	2nwaE01	E:2-77
1f	2nwaF01	F:2-77
1g	2nwaG01	G:2-77
1h	2nwaH01	H:2-77

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: no clan defined [family: DUF2584] (1)

Family: DUF2584 (1)

Bacillus subtilis (1)

1a	DUF2584-2nwaH01	H:1-80
1b	DUF2584-2nwaH02	H:1-80
1c	DUF2584-2nwaH03	H:1-80
1d	DUF2584-2nwaH04	H:1-80
1e	DUF2584-2nwaH05	H:1-80
1f	DUF2584-2nwaH06	H:1-80
1g	DUF2584-2nwaH07	H:1-80
1h	DUF2584-2nwaH08	H:1-80

Asymmetric Unit(hide GO term definitions)

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Description

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Ligands, Modified Residues, Ions (2, 40)

Sites (8, 8)

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