1VI6 - JenaLib

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Title :   CRYSTAL STRUCTURE OF RIBOSOMAL PROTEIN S2P

Authors :   Structural Genomix

Date :   01 Dec 03 (Deposition) - 30 Dec 03 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.95

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

Keywords :   Structural Genomics, Ribosome (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. Badger, J. M. Sauder, J. M. Adams, S. Antonysamy, K. Bain, M. G. Bergseid, S. G. Buchanan, M. D. Buchanan, Y. Batiyenko, J. A. Christopher, S. Emtage, A. Eroshkina, I. Feil, E. B. Furlong, K. S. Gajiwala, X. Gao, D. He, J. Hendle, A. Huber, K. Hoda, P. Kearins, C. Kissinger, B. Laubert, H. A. Lewis, J. Lin, K. Loomis, D. Lorimer, G. Louie, M. Maletic, C. D. Marsh, I. Miller, J. Molinari, H. J. Muller-Dieckmann, J. M. Newman, B. W. Noland, B. Pagarigan, F. Park, T. S. Peat, K. W. Post, S. Radojicic, A. Ramos, R. Romero, M. E. Rutter, W. E. Sanderson, K. D. Schwinn, J. Tresser, J. Winhoven, T. A. Wright, L. Wu, J. Xu, T. J. Harris
Structural Analysis Of A Set Of Proteins Resulting From A Bacterial Genomics Project
Proteins V. 60 787 2005
PubMed-ID: 16021622 | Reference-DOI: 10.1002/PROT.20541
(for further references see the PDB file header)

Molecule 1 - 30S RIBOSOMAL PROTEIN S2P
	Chains	:	A, B, C, D
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Gene	:	RPS2P, AF1133
	Organism Scientific	:	ARCHAEOGLOBUS FULGIDUS
	Organism Taxid	:	2234

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 10)

No.	Name	Count	Type	Full Name
1	NA	10	Ligand/Ion	SODIUM ION

Biological Unit 1 (0, 0)

No.	Name	Count	Type	Full Name
1	NA	-1	Ligand/Ion	SODIUM ION

Biological Unit 2 (0, 0)

No.	Name	Count	Type	Full Name
1	NA	-1	Ligand/Ion	SODIUM ION

Asymmetric Unit (10, 10)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	THR D:134 , VAL D:140 , ASP D:152 , ASP D:154 , HOH D:224 , HOH D:226	BINDING SITE FOR RESIDUE NA D 208
02	AC2	SOFTWARE	THR A:134 , VAL A:140 , ASP A:152 , ASP A:154 , HOH A:232 , HOH A:261	BINDING SITE FOR RESIDUE NA A 208
03	AC3	SOFTWARE	THR B:134 , VAL B:140 , ASP B:152 , ASP B:154 , HOH B:221 , HOH B:233	BINDING SITE FOR RESIDUE NA B 208
04	AC4	SOFTWARE	ILE C:22 , GLY C:23 , ASP C:145 , ASN C:160 , HOH C:356	BINDING SITE FOR RESIDUE NA C 208
05	AC5	SOFTWARE	THR C:134 , VAL C:140 , ASP C:152 , ASP C:154 , HOH C:226 , HOH C:234	BINDING SITE FOR RESIDUE NA C 209
06	AC6	SOFTWARE	ILE A:22 , GLY A:23 , ASP A:145 , ASN A:160 , HOH A:357	BINDING SITE FOR RESIDUE NA A 209
07	AC7	SOFTWARE	ILE D:22 , GLY D:23 , ASP D:145 , ASN D:160 , HOH D:332	BINDING SITE FOR RESIDUE NA D 209
08	AC8	SOFTWARE	ILE B:22 , GLY B:23 , ASP B:145 , ASN B:160 , HOH B:336	BINDING SITE FOR RESIDUE NA B 209
09	AC9	SOFTWARE	HOH B:334 , PHE C:186 , HOH C:261 , HOH C:282 , HOH C:357	BINDING SITE FOR RESIDUE NA C 210
10	BC1	SOFTWARE	PHE A:186 , HOH A:274 , HOH A:351 , HOH A:365 , HOH A:366	BINDING SITE FOR RESIDUE NA A 210

(no "SS Bond" information available for 1VI6)

(no "Cis Peptide Bond" information available for 1VI6)

(no "SAP(SNP)/Variant" information available for 1VI6)

Asymmetric Unit (1, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	RIBOSOMAL_S2_2	PS00963	Ribosomal protein S2 signature 2.	RS2_ARCFU	115-139	4	A:115-139 B:115-139 C:115-139 D:115-139

Biological Unit 1 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	RIBOSOMAL_S2_2	PS00963	Ribosomal protein S2 signature 2.	RS2_ARCFU	115-139	2	A:115-139 B:115-139 - -

Biological Unit 2 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	RIBOSOMAL_S2_2	PS00963	Ribosomal protein S2 signature 2.	RS2_ARCFU	115-139	2	- - C:115-139 D:115-139

(no "Exon" information available for 1VI6)

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:193
 aligned with RS2_ARCFU | O29132 from UniProtKB/Swiss-Prot  Length:197

    Alignment length:193
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194   
            RS2_ARCFU     5 EYEYLVPPDDYLAAGVHIGTQIKTGDMKKFIFKVRQDGLYVLDIRKLDERIRVAAKFLSRYEPSKILLVAARQYAHKPVQMFSKVVGSDYIVGRFIPGTLTNPMLSEYREPEVVFVNDPAIDKQAVSEATAVGIPVVALCDSNNSSADVDLVIPTNNKGRRALAIVYWLLAREIAKIRGQDFTYSIEDFEAEL 197
               SCOP domains d1vi6a_ A: Ribosomal protein S2                                                                                                                                                                   SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhhhhhh...........hhh.eeee.....eeehhhhhhhhhhhhhhhhhhhhhh.eeeee.hhhhhhhhhhhhhhhh.eeee....................eeee.....hhhhhhhhhhh...eeeee..........eeee....hhhhhhhhhhhhhhhhhhhhh.....hhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------RIBOSOMAL_S2_2           ---------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1vi6 A   5 EYEYLVPPDDYLAAGVHIGTQIKTGDMKKFIFKVRQDGLYVLDIRKLDERIRVAAKFLSRYEPSKILLVAARQYAHKPVQMFSKVVGSDYIVGRFIPGTLTNPMLSEYREPEVVFVNDPAIDKQAVSEATAVGIPVVALCDSNNSSADVDLVIPTNNKGRRALAIVYWLLAREIAKIRGQDFTYSIEDFEAEL 197
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194

Chain B from PDB  Type:PROTEIN  Length:193
 aligned with RS2_ARCFU | O29132 from UniProtKB/Swiss-Prot  Length:197

    Alignment length:193
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194   
            RS2_ARCFU     5 EYEYLVPPDDYLAAGVHIGTQIKTGDMKKFIFKVRQDGLYVLDIRKLDERIRVAAKFLSRYEPSKILLVAARQYAHKPVQMFSKVVGSDYIVGRFIPGTLTNPMLSEYREPEVVFVNDPAIDKQAVSEATAVGIPVVALCDSNNSSADVDLVIPTNNKGRRALAIVYWLLAREIAKIRGQDFTYSIEDFEAEL 197
               SCOP domains d1vi6b_ B: Ribosomal protein S2                                                                                                                                                                   SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhhhhhh...........hhh.eeee.....eeehhhhhhhhhhhhhhhhhhhhhh.eeeee.hhhhhhhhhhhhhhhh.eeee....................eeee.....hhhhhhhhhhh...eeeee..........eeee....hhhhhhhhhhhhhhhhhhhhh......hhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------RIBOSOMAL_S2_2           ---------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1vi6 B   5 EYEYLVPPDDYLAAGVHIGTQIKTGDMKKFIFKVRQDGLYVLDIRKLDERIRVAAKFLSRYEPSKILLVAARQYAHKPVQMFSKVVGSDYIVGRFIPGTLTNPMLSEYREPEVVFVNDPAIDKQAVSEATAVGIPVVALCDSNNSSADVDLVIPTNNKGRRALAIVYWLLAREIAKIRGQDFTYSIEDFEAEL 197
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194

Chain C from PDB  Type:PROTEIN  Length:194
 aligned with RS2_ARCFU | O29132 from UniProtKB/Swiss-Prot  Length:197

    Alignment length:194
                                                                                                                                                                                                                          197 
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194  | 
            RS2_ARCFU     5 EYEYLVPPDDYLAAGVHIGTQIKTGDMKKFIFKVRQDGLYVLDIRKLDERIRVAAKFLSRYEPSKILLVAARQYAHKPVQMFSKVVGSDYIVGRFIPGTLTNPMLSEYREPEVVFVNDPAIDKQAVSEATAVGIPVVALCDSNNSSADVDLVIPTNNKGRRALAIVYWLLAREIAKIRGQDFTYSIEDFEAEL-   -
               SCOP domains d1vi6c_ C: Ribosomal protein S2                                                                                                                                                                    SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhhhhhh...........hhh.eeee.....eeehhhhhhhhhhhhhhhhhhhhhh.eeeee.hhhhhhhhhhhhhhhh.eeee....................eeee.....hhhhhhhhhhh...eeeee..........eeee....hhhhhhhhhhhhhhhhhhhhh.....hhhhhh.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------RIBOSOMAL_S2_2           ----------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1vi6 C   5 EYEYLVPPDDYLAAGVHIGTQIKTGDMKKFIFKVRQDGLYVLDIRKLDERIRVAAKFLSRYEPSKILLVAARQYAHKPVQMFSKVVGSDYIVGRFIPGTLTNPMLSEYREPEVVFVNDPAIDKQAVSEATAVGIPVVALCDSNNSSADVDLVIPTNNKGRRALAIVYWLLAREIAKIRGQDFTYSIEDFEAELE 198
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194

Chain D from PDB  Type:PROTEIN  Length:193
 aligned with RS2_ARCFU | O29132 from UniProtKB/Swiss-Prot  Length:197

    Alignment length:193
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194   
            RS2_ARCFU     5 EYEYLVPPDDYLAAGVHIGTQIKTGDMKKFIFKVRQDGLYVLDIRKLDERIRVAAKFLSRYEPSKILLVAARQYAHKPVQMFSKVVGSDYIVGRFIPGTLTNPMLSEYREPEVVFVNDPAIDKQAVSEATAVGIPVVALCDSNNSSADVDLVIPTNNKGRRALAIVYWLLAREIAKIRGQDFTYSIEDFEAEL 197
               SCOP domains d1vi6d_ D: Ribosomal protein S2                                                                                                                                                                   SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ------------------------------------------------------------------------------------------------------Ribosomal_S2-1vi6D01 D:107-182                                              --------------- Pfam domains (1)
           Pfam domains (2) ------------------------------------------------------------------------------------------------------Ribosomal_S2-1vi6D02 D:107-182                                              --------------- Pfam domains (2)
           Pfam domains (3) ------------------------------------------------------------------------------------------------------Ribosomal_S2-1vi6D03 D:107-182                                              --------------- Pfam domains (3)
           Pfam domains (4) ------------------------------------------------------------------------------------------------------Ribosomal_S2-1vi6D04 D:107-182                                              --------------- Pfam domains (4)
           Pfam domains (5) ------------------------------------------------------------------------------------------------------Ribosomal_S2-1vi6D05 D:107-182                                              --------------- Pfam domains (5)
           Pfam domains (6) ------------------------------------------------------------------------------------------------------Ribosomal_S2-1vi6D06 D:107-182                                              --------------- Pfam domains (6)
           Pfam domains (7) ------------------------------------------------------------------------------------------------------Ribosomal_S2-1vi6D07 D:107-182                                              --------------- Pfam domains (7)
           Pfam domains (8) ------------------------------------------------------------------------------------------------------Ribosomal_S2-1vi6D08 D:107-182                                              --------------- Pfam domains (8)
         Sec.struct. author ......hhhhhhhhh...........hhh.eeee.....eeehhhhhhhhhhhhhhhhhhhhhh.eeeee.hhhhhhhhhhhhhhhh.eeee....................eeee.....hhhhhhhhhhh...eeeee..........eeee....hhhhhhhhhhhhhhhhhhhhh.....hhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------RIBOSOMAL_S2_2           ---------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1vi6 D   5 EYEYLVPPDDYLAAGVHIGTQIKTGDMKKFIFKVRQDGLYVLDIRKLDERIRVAAKFLSRYEPSKILLVAARQYAHKPVQMFSKVVGSDYIVGRFIPGTLTNPMLSEYREPEVVFVNDPAIDKQAVSEATAVGIPVVALCDSNNSSADVDLVIPTNNKGRRALAIVYWLLAREIAKIRGQDFTYSIEDFEAEL 197
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194

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

Fold: Flavodoxin-like (1057)

Superfamily: Ribosomal protein S2 (74)

Family: Ribosomal protein S2 (74)

Protein domain: Ribosomal protein S2 (74)

Archaeoglobus fulgidus [TaxId: 2234] (2)

1a	d1vi6a_	A:
1b	d1vi6b_	B:
1c	d1vi6c_	C:
1d	d1vi6d_	D:

(no "CATH Domain" information available for 1VI6)

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D (RS2_ARCFU | O29132)

molecular function
	GO:0003735	structural constituent of ribosome	The action of a molecule that contributes to the structural integrity of the ribosome.
biological process
	GO:0006412	translation	The cellular metabolic process in which a protein is formed, using the sequence of a mature mRNA or circRNA molecule to specify the sequence of amino acids in a polypeptide chain. Translation is mediated by the ribosome, and begins with the formation of a ternary complex between aminoacylated initiator methionine tRNA, GTP, and initiation factor 2, which subsequently associates with the small subunit of the ribosome and an mRNA or circRNA. Translation ends with the release of a polypeptide chain from the ribosome.
cellular component
	GO:0005622	intracellular	The living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm.
	GO:0030529	intracellular ribonucleoprotein complex	An intracellular macromolecular complex containing both protein and RNA molecules.
	GO:0005840	ribosome	An intracellular organelle, about 200 A in diameter, consisting of RNA and protein. It is the site of protein biosynthesis resulting from translation of messenger RNA (mRNA). It consists of two subunits, one large and one small, each containing only protein and RNA. Both the ribosome and its subunits are characterized by their sedimentation coefficients, expressed in Svedberg units (symbol: S). Hence, the prokaryotic ribosome (70S) comprises a large (50S) subunit and a small (30S) subunit, while the eukaryotic ribosome (80S) comprises a large (60S) subunit and a small (40S) subunit. Two sites on the ribosomal large subunit are involved in translation, namely the aminoacyl site (A site) and peptidyl site (P site). Ribosomes from prokaryotes, eukaryotes, mitochondria, and chloroplasts have characteristically distinct ribosomal proteins.
	GO:0015935	small ribosomal subunit	The smaller of the two subunits of a ribosome.

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	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1vi6)

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(no "Related Entries Specified in the PDB File" available for 1VI6)

Description

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SS Bonds (0, 0)

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