2RA2 - JenaLib

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Title :   X-RAY STRUCTURE OF THE Q7CPV8 PROTEIN FROM SALMONELLA TYPHIMURIUM AT THE RESOLUTION 1.9 A. NORTHEAST STRUCTURAL GENOMICS CONSORTIUM TARGET STR88A

Authors :   A. P. Kuzin, M. Su, J. Seetharaman, S. M. Vorobiev, H. Wang, L. Mao, K. Cunningham, R. Xiao, J. Liu, M. C. Baran, T. B. Acton, B. Rost, G. T. Montelione, J. F. Hunt, L. Tong, Northeast Structural Genomics Consortium (Nesg)

Date :   14 Sep 07 (Deposition) - 09 Oct 07 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.90

Chains :   Asym. Unit : A,B,C,D,E,F
Biol. Unit 1: A  (1x)
Biol. Unit 2: B  (1x)
Biol. Unit 3: C  (1x)
Biol. Unit 4: D  (1x)
Biol. Unit 5: E  (1x)
Biol. Unit 6: F  (1x)
Biol. Unit 7: A,B,F  (2x)
Biol. Unit 8: C,D,E  (2x)

Keywords :   X-Ray, Nesg, Str88A, Q7Cpv8, Structural Genomics, Psi-2, Protein Structure Initiative, Northeast Structural Genomics Consortium, Lipoprotein, Unknown Function (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   A. P. Kuzin, M. Su, J. Seetharaman, S. M. Vorobiev, H. Wang, L. Mao, K. Cunningham, R. Xiao, J. Liu, M. C. Baran, T. B. Acton, B. Rost, G. T. Montelione, J. F. Hunt, L. Tong
X-Ray Structure Of The Q7Cpv8 Protein From Salmonella Typhimurium At The Resolution 1. 9 A.
To Be Published
PubMed: search
(for further references see the PDB file header)

Molecule 1 - PUTATIVE LIPOPROTEIN
	Atcc	:	700720
	Chains	:	A, B, C, D, E, F
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Fragment	:	RESIDUES 21-75
	Gene	:	YGDI, STM2983
	Organism Scientific	:	SALMONELLA TYPHIMURIUM LT2
	Organism Taxid	:	99287
	Strain	:	SGSC1412

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 19)

No.	Name	Count	Type	Full Name
1	MSE	19	Mod. Amino Acid	SELENOMETHIONINE

Biological Unit 1 (1, 3)

No.	Name	Count	Type	Full Name
1	MSE	3	Mod. Amino Acid	SELENOMETHIONINE

Biological Unit 2 (1, 4)

No.	Name	Count	Type	Full Name
1	MSE	4	Mod. Amino Acid	SELENOMETHIONINE

Biological Unit 3 (1, 3)

No.	Name	Count	Type	Full Name
1	MSE	3	Mod. Amino Acid	SELENOMETHIONINE

Biological Unit 4 (1, 3)

No.	Name	Count	Type	Full Name
1	MSE	3	Mod. Amino Acid	SELENOMETHIONINE

Biological Unit 5 (1, 3)

No.	Name	Count	Type	Full Name
1	MSE	3	Mod. Amino Acid	SELENOMETHIONINE

Biological Unit 6 (1, 3)

No.	Name	Count	Type	Full Name
1	MSE	3	Mod. Amino Acid	SELENOMETHIONINE

Biological Unit 7 (1, 20)

No.	Name	Count	Type	Full Name
1	MSE	20	Mod. Amino Acid	SELENOMETHIONINE

Biological Unit 8 (1, 18)

No.	Name	Count	Type	Full Name
1	MSE	18	Mod. Amino Acid	SELENOMETHIONINE

(no "Site" information available for 2RA2)

(no "SS Bond" information available for 2RA2)

(no "Cis Peptide Bond" information available for 2RA2)

(no "SAP(SNP)/Variant" information available for 2RA2)

(no "PROSITE Motif" information available for 2RA2)

(no "Exon" information available for 2RA2)

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:55
 aligned with Q7CPV8_SALTY | Q7CPV8 from UniProtKB/TrEMBL  Length:75

    Alignment length:55
                                                                               75  
                                    32        42        52        62        72  |  
          Q7CPV8_SALTY   23 PNYVMHTNDGRSIVTDGKPQTDNDTGMISYKDANGNKQQINRTDVKEMVALEN--  -
               SCOP domains d2ra2a1 A:4-56 Uncharacterized protein YgdI          -- SCOP domains
               CATH domains 2ra2A00 A:4-58  [code=2.30.30.100, no name defined]     CATH domains
               Pfam domains ------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee....eee.....ee......eeee.....eeeehhh.eeeeee..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------- Transcript
                  2ra2 A  4 PNYVmHTNDGRSIVTDGKPQTDNDTGmISYKDANGNKQQINRTDVKEmVALENLE 58
                                |   13        23      | 33        43       |53     
                                |                    30-MSE               51-MSE   
                                8-MSE

Chain B from PDB  Type:PROTEIN  Length:59
 aligned with Q7CPV8_SALTY | Q7CPV8 from UniProtKB/TrEMBL  Length:75

    Alignment length:59
                                                                                  75   
                                    29        39        49        59        69     |   
          Q7CPV8_SALTY   20 CSGPNYVMHTNDGRSIVTDGKPQTDNDTGMISYKDANGNKQQINRTDVKEMVALEN---  -
               SCOP domains d2ra2b_ B: Uncharacterized protein YgdI                     SCOP domains
               CATH domains -2ra2B00 B:2-59  [code=2.30.30.100, no name defined]        CATH domains
               Pfam domains ----------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeee....eeeee...ee......eeee.....eeee....eeeee....... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------- Transcript
                  2ra2 B  1 mSGPNYVmHTNDGRSIVTDGKPQTDNDTGmISYKDANGNKQQINRTDVKEmVALENLEH 59
                            |      |10        20        30        40        50|        
                            1-MSE  8-MSE                30-MSE               51-MSE

Chain C from PDB  Type:PROTEIN  Length:55
 aligned with Q7CPV8_SALTY | Q7CPV8 from UniProtKB/TrEMBL  Length:75

    Alignment length:55
                                                                                75 
                                    31        41        51        61        71   | 
          Q7CPV8_SALTY   22 GPNYVMHTNDGRSIVTDGKPQTDNDTGMISYKDANGNKQQINRTDVKEMVALEN-  -
               SCOP domains d2ra2c_ C: Uncharacterized protein YgdI                 SCOP domains
               CATH domains 2ra2C00 C:3-57  [code=2.30.30.100, no name defined]     CATH domains
               Pfam domains ------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee....eeeee...ee......eeee.....eeee....eeeeee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------- Transcript
                  2ra2 C  3 GPNYVmHTNDGRSIVTDGKPQTDNDTGmISYKDANGNKQQINRTDVKEmVALENL 57
                                 |  12        22       |32        42        52     
                                 8-MSE                30-MSE               51-MSE

Chain D from PDB  Type:PROTEIN  Length:55
 aligned with Q7CPV8_SALTY | Q7CPV8 from UniProtKB/TrEMBL  Length:75

    Alignment length:55
                                    30        40        50        60        70     
          Q7CPV8_SALTY   21 SGPNYVMHTNDGRSIVTDGKPQTDNDTGMISYKDANGNKQQINRTDVKEMVALEN 75
               SCOP domains d2ra2d_ D: Uncharacterized protein YgdI                 SCOP domains
               CATH domains 2ra2D00 D:2-56  [code=2.30.30.100, no name defined]     CATH domains
               Pfam domains ------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeee....eeee....ee......eeee.....eeee....eeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------- Transcript
                  2ra2 D  2 SGPNYVmHTNDGRSIVTDGKPQTDNDTGmISYKDANGNKQQINRTDVKEmVALEN 56
                                  | 11        21        31        41        51     
                                  8-MSE                30-MSE               51-MSE

Chain E from PDB  Type:PROTEIN  Length:53
 aligned with Q7CPV8_SALTY | Q7CPV8 from UniProtKB/TrEMBL  Length:75

    Alignment length:53
                                    32        42        52        62        72   
          Q7CPV8_SALTY   23 PNYVMHTNDGRSIVTDGKPQTDNDTGMISYKDANGNKQQINRTDVKEMVALEN 75
               SCOP domains d2ra2e_ E: Uncharacterized protein YgdI               SCOP domains
               CATH domains 2ra2E00 E:4-56  [code=2.30.30.100, no name defined]   CATH domains
               Pfam domains ----------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee....eeee....ee......eeee.....eeeehhh.eeeeee... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------- Transcript
                  2ra2 E  4 PNYVmHTNDGRSIVTDGKPQTDNDTGmISYKDANGNKQQINRTDVKEmVALEN 56
                                |   13        23      | 33        43       |53   
                                8-MSE                30-MSE               51-MSE

Chain F from PDB  Type:PROTEIN  Length:53
 aligned with Q7CPV8_SALTY | Q7CPV8 from UniProtKB/TrEMBL  Length:75

    Alignment length:53
                                    31        41        51        61        71   
          Q7CPV8_SALTY   22 GPNYVMHTNDGRSIVTDGKPQTDNDTGMISYKDANGNKQQINRTDVKEMVALE 74
               SCOP domains d2ra2f_ F: Uncharacterized protein YgdI               SCOP domains
               CATH domains 2ra2F00 F:3-55  [code=2.30.30.100, no name defined]   CATH domains
           Pfam domains (1) --DUF903-2ra2F01 F:5-54                             - Pfam domains (1)
           Pfam domains (2) --DUF903-2ra2F02 F:5-54                             - Pfam domains (2)
           Pfam domains (3) --DUF903-2ra2F03 F:5-54                             - Pfam domains (3)
           Pfam domains (4) --DUF903-2ra2F04 F:5-54                             - Pfam domains (4)
           Pfam domains (5) --DUF903-2ra2F05 F:5-54                             - Pfam domains (5)
           Pfam domains (6) --DUF903-2ra2F06 F:5-54                             - Pfam domains (6)
         Sec.struct. author ..eeeeee....eeeee...ee......eeee.....eeee....eeeeee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------- Transcript
                  2ra2 F  3 GPNYVmHTNDGRSIVTDGKPQTDNDTGmISYKDANGNKQQINRTDVKEmVALE 55
                                 |  12        22       |32        42        52   
                                 8-MSE                30-MSE               51-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(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: All beta proteins (24004)

Fold: Sm-like fold (103)

Superfamily: Sm-like ribonucleoproteins (95)

Family: YgdI/YgdR-like (7)

Protein domain: Uncharacterized protein YgdI (1)

Salmonella typhimurium [TaxId: 90371] (1)

1a	d2ra2a1	A:4-56
1b	d2ra2b_	B:
1c	d2ra2c_	C:
1d	d2ra2d_	D:
1e	d2ra2e_	E:
1f	d2ra2f_	F:

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Beta (13760)

Architecture: Roll (1513)

Topology: SH3 type barrels. (648)

Homologous Superfamily: [code=2.30.30.100, no name defined] (40)

Salmonella typhimurium lt2. Organism_taxid: 99287. Strain: sgsc1412. (1)

1a	2ra2B00	B:2-59
1b	2ra2A00	A:4-58
1c	2ra2C00	C:3-57
1d	2ra2D00	D:2-56
1e	2ra2E00	E:4-56
1f	2ra2F00	F:3-55

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: no clan defined [family: DUF903] (4)

Family: DUF903 (4)

Salmonella typhimurium (1)

1a	DUF903-2ra2F01	F:5-54
1b	DUF903-2ra2F02	F:5-54
1c	DUF903-2ra2F03	F:5-54
1d	DUF903-2ra2F04	F:5-54
1e	DUF903-2ra2F05	F:5-54
1f	DUF903-2ra2F06	F:5-54

Asymmetric Unit(hide GO term definitions)

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2jn0	SOLUTION NMR STRUCTURE OF THE YGDR PROTEIN FROM ESCHERICHIA COLI (A HOMOLOG)

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