1NS5 - JenaLib

Asym./Biol. Unit (Jmol Viewer)

Title :   X-RAY STRUCTURE OF YBEA FROM E.COLI. NORTHEAST STRUCTURAL GENOMICS RESEARCH CONSORTIUM (NESG) TARGET ER45

Authors :   J. Benach, J. Shen, B. Rost, R. Xiao, T. Acton, G. Montelione, J. F. Hunt, Northeast Structural Genomics Consortium (Nesg)

Date :   27 Jan 03 (Deposition) - 04 Feb 03 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.68

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

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

Reference :   J. Benach, J. Shen, B. Rost, R. Xiao, T. Acton, G. Montelione, J. F. Hunt
Structure Of Ybea From E. Coli
To Be Published
PubMed: search
(for further references see the PDB file header)

Molecule 1 - HYPOTHETICAL PROTEIN YBEA
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Gene	:	YBEA
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	562

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (1, 8)

No.	Name	Count	Type	Full Name
1	MSE	8	Mod. Amino Acid	SELENOMETHIONINE

(no "Site" information available for 1NS5)

(no "SS Bond" information available for 1NS5)

(no "Cis Peptide Bond" information available for 1NS5)

(no "SAP(SNP)/Variant" information available for 1NS5)

(no "PROSITE Motif" information available for 1NS5)

(no "Exon" information available for 1NS5)

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
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Chain A from PDB  Type:PROTEIN  Length:153
 aligned with RLMH_ECOLI | P0A8I8 from UniProtKB/Swiss-Prot  Length:155

    Alignment length:153
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150   
           RLMH_ECOLI     1 MKLQLVAVGTKMPDWVQTGFTEYLRRFPKDMPFELIEIPAGKRGKNADIKRILDKEGEQMLAAAGKNRIVTLDIPGKPWDTPQLAAELERWKLDGRDVSLLIGGPEGLSPACKAAAEQSWSLSALTLPHPLVRVLVAESLYRAWSITTNHPYH 153
               SCOP domains d1ns5a_ A: Hypothetical protein YbeA                                                                                                                      SCOP domains
               CATH domains -1ns5A00 A:2-153  [code=3.40.1280.10, no name defined]                                                                                                    CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee....hhhhhhhhhhhhh.......eeeeee.........hhhhhhhhhhhhhhhhhh..eeeee.......hhhhhhhhhhhhhhhh..eeeee......hhhhhhhh.eee.......hhhhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ns5 A   1 mKLQLVAVGTKmPDWVQTGFTEYLRRFPKDmPFELIEIPAGKRGKNADIKRILDKEGEQmLAAAGKNRIVTLDIPGKPWDTPQLAAELERWKLDGRDVSLLIGGPEGLSPACKAAAEQSWSLSALTLPHPLVRVLVAESLYRAWSITTNHPYH 153
                            |       10 |      20        30|       40        50        60        70        80        90       100       110       120       130       140       150   
                            |         12-MSE             31-MSE                       60-MSE                                                                                         
                            1-MSE

Chain B from PDB  Type:PROTEIN  Length:155
 aligned with RLMH_ECOLI | P0A8I8 from UniProtKB/Swiss-Prot  Length:155

    Alignment length:155
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150     
           RLMH_ECOLI     1 MKLQLVAVGTKMPDWVQTGFTEYLRRFPKDMPFELIEIPAGKRGKNADIKRILDKEGEQMLAAAGKNRIVTLDIPGKPWDTPQLAAELERWKLDGRDVSLLIGGPEGLSPACKAAAEQSWSLSALTLPHPLVRVLVAESLYRAWSITTNHPYHRE 155
               SCOP domains d1ns5b_ B: Hypothetical protein YbeA                                                                                                                        SCOP domains
               CATH domains -1ns5B00 B:2-155  [code=3.40.1280.10, no name defined]                                                                                                      CATH domains
           Pfam domains (1) SPOUT_MTase-1ns5B01 B:1-153                                                                                                                              -- Pfam domains (1)
           Pfam domains (2) SPOUT_MTase-1ns5B02 B:1-153                                                                                                                              -- Pfam domains (2)
         Sec.struct. author ..eeeeee....hhhhhhhhhhhhh.......eeeeee.........hhhhhhhhhhhhhhhhhh..eeeee.......hhhhhhhhhhhhhh....eeeee......hhhhhhhh.eee.......hhhhhhhhhhhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ns5 B   1 mKLQLVAVGTKmPDWVQTGFTEYLRRFPKDmPFELIEIPAGKRGKNADIKRILDKEGEQmLAAAGKNRIVTLDIPGKPWDTPQLAAELERWKLDGRDVSLLIGGPEGLSPACKAAAEQSWSLSALTLPHPLVRVLVAESLYRAWSITTNHPYHRE 155
                            |       10 |      20        30|       40        50        60        70        80        90       100       110       120       130       140       150     
                            1-MSE     12-MSE             31-MSE                       60-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(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

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

Fold: alpha/beta knot (57)

Superfamily: alpha/beta knot (57)

Family: YbeA-like (5)

Protein domain: Hypothetical protein YbeA (1)

Escherichia coli [TaxId: 562] (1)

1a	d1ns5a_	A:
1b	d1ns5b_	B:

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

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

Topology: Alpha/beta knot (33)

Homologous Superfamily: [code=3.40.1280.10, no name defined] (33)

Escherichia coli. Organism_taxid: 562. (1)

1a	1ns5B00	B:2-155
1b	1ns5A00	A:2-153

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: SPOUT (28)

Family: SPOUT_MTase (3)

Escherichia coli (strain K12) (1)

1a	SPOUT_MTase-1ns5B01	B:1-153
1b	SPOUT_MTase-1ns5B02	B:1-153

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (RLMH_ECOLI | P0A8I8)

molecular function
	GO:0008168	methyltransferase activity	Catalysis of the transfer of a methyl group to an acceptor molecule.
	GO:0042803	protein homodimerization activity	Interacting selectively and non-covalently with an identical protein to form a homodimer.
	GO:0070038	rRNA (pseudouridine-N3-)-methyltransferase activity	Catalysis of the reaction: S-adenosyl-L-methionine + rRNA = S-adenosyl-L-homocysteine + rRNA containing N3-methylpseudouridine.
	GO:0043022	ribosome binding	Interacting selectively and non-covalently with any part of a ribosome.
	GO:0016740	transferase activity	Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
biological process
	GO:0032259	methylation	The process in which a methyl group is covalently attached to a molecule.
	GO:0070475	rRNA base methylation	The addition of a methyl group to an atom in the nucleoside base portion of a nucleotide residue in an rRNA molecule.
	GO:0031167	rRNA methylation	The posttranscriptional addition of methyl groups to specific residues in an rRNA molecule.
	GO:0006364	rRNA processing	Any process involved in the conversion of a primary ribosomal RNA (rRNA) transcript into one or more mature rRNA molecules.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

Asymmetric/Biological Unit
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Description

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Ligands, Modified Residues, Ions (1, 8)

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SS Bonds (0, 0)

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