1NXZ - JenaLib

Asym./Biol. Unit (Jmol Viewer)

Title :   X-RAY CRYSTAL STRUCTURE OF PROTEIN YGGJ_HAEIN OF HAEMOPHILUS INFLUENZAE. NORTHEAST STRUCTURAL GENOMICS CONSORTIUM TARGET IR73.

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

Date :   11 Feb 03 (Deposition) - 11 Mar 03 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.00

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

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

Reference :   F. Forouhar, J. Shen, R. Xiao, T. B. Acton, G. T. Montelione, L. Tong
Functional Assignment Based On Structural Analysis: Crystal Structure Of The Yggj Protein (Hi0303) Of Haemophilus Influenzae Reveals An Rna Methyltransferase With A Deep Trefoil Knot.
Proteins V. 53 329 2003
PubMed-ID: 14517985 | Reference-DOI: 10.1002/PROT.10510
(for further references see the PDB file header)

Molecule 1 - HYPOTHETICAL PROTEIN HI0303
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Gene	:	HI0303
	Organism Scientific	:	HAEMOPHILUS INFLUENZAE
	Organism Taxid	:	727

		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 1NXZ)

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

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

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

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

(no "Exon" information available for 1NXZ)

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
	(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:246
 aligned with RSME_HAEIN | P44627 from UniProtKB/Swiss-Prot  Length:245

    Alignment length:246
                                                                                                                                                                                                                                                                             245  
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241   |  
           RSME_HAEIN     2 RIPRIYHPISLENQTQCYLSEDAANHVARVLRMTEGEQLELFDGSNHIYPAKIIESNKKSVKVEILGRELADKESHLKIHLGQVISRGERMEFTIQKSVELGVNVITPLWSERCGVKLDAERMDKKIQQWQKIAIAACEQCGRNIVPEIRPLMKLQDWCAENDGALKLNLHPRAHYSIKTLPTIPAGGVRLLIGSEGGLSAQEIAQTEQQGFTEILLGKRVLRTETASLAAISALQICFGDLGE--   -
               SCOP domains d1nxza1 A:2-73 Hypothetical protein HI0303                              d1nxza2 A:74-247 Hypothetical protein HI0303                                                                                                                                   SCOP domains
               CATH domains 1nxzA01 A:2-73 Hypothetical PUA domain-like; domain 1                   1nxzA02 A:74-247  [code=3.40.1280.10, no name defined]                                                                                                                         CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eee.........eee.hhhhhhhhhh........eeeee....eeeeeeeeeee..eeeeee...ee........eeeeee.....hhhhhhhhhhhh...eeeeee........hhhhhhhhhhhhhhhhhhhhhhhh.....ee...eehhhhhhh....eeeee......hhhhh.......eeeee......hhhhhhhhhhh..eee.......hhhhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1nxz A   2 RIPRIYHPISLENQTQCYLSEDAANHVARVLRmTEGEQLELFDGSNHIYPAKIIESNKKSVKVEILGRELADKESHLKIHLGQVISRGERmEFTIQKSVELGVNVITPLWSERCGVKLDAERmDKKIQQWQKIAIAACEQCGRNIVPEIRPLmKLQDWCAENDGALKLNLHPRAHYSIKTLPTIPAGGVRLLIGSEGGLSAQEIAQTEQQGFTEILLGKRVLRTETASLAAISALQICFGDLGEAA 247
                                    11        21        31  |     41        51        61        71        81        91|      101       111       121  |    131       141       151  |    161       171       181       191       201       211       221       231       241      
                                                           34-MSE                                                    92-MSE                         124-MSE                       154-MSE

Chain B from PDB  Type:PROTEIN  Length:245
 aligned with RSME_HAEIN | P44627 from UniProtKB/Swiss-Prot  Length:245

    Alignment length:245
                                                                                                                                                                                                                                                                             245 
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241   | 
           RSME_HAEIN     2 RIPRIYHPISLENQTQCYLSEDAANHVARVLRMTEGEQLELFDGSNHIYPAKIIESNKKSVKVEILGRELADKESHLKIHLGQVISRGERMEFTIQKSVELGVNVITPLWSERCGVKLDAERMDKKIQQWQKIAIAACEQCGRNIVPEIRPLMKLQDWCAENDGALKLNLHPRAHYSIKTLPTIPAGGVRLLIGSEGGLSAQEIAQTEQQGFTEILLGKRVLRTETASLAAISALQICFGDLGE-   -
               SCOP domains d1nxzb1 B:2-73 Hypothetical protein HI0303                              d1nxzb2 B:74-246 Hypothetical protein HI0303                                                                                                                                  SCOP domains
               CATH domains 1nxzB01 B:2-73 Hypothetical PUA domain-like; domain 1                   1nxzB02 B:74-246  [code=3.40.1280.10, no name defined]                                                                                                                        CATH domains
           Pfam domains (1) ----------------Methyltrans_RNA-1nxzB01 B:18-238                                                                                                                                                                                             -------- Pfam domains (1)
           Pfam domains (2) ----------------Methyltrans_RNA-1nxzB02 B:18-238                                                                                                                                                                                             -------- Pfam domains (2)
         Sec.struct. author ...eee.........eee.hhhhhhhhhhh.......eeeee....eeeeeeeeee....eeeee...ee........eeeeee.....hhhhhhhhhhhh...eeeeee........hhhhhhhhhhhhhhhhhhhhhhhh.....ee...eehhhhhh.....eeeee.....ee.hhh.......eeeee........hhhhhhhhh..eeee......hhhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1nxz B   2 RIPRIYHPISLENQTQCYLSEDAANHVARVLRmTEGEQLELFDGSNHIYPAKIIESNKKSVKVEILGRELADKESHLKIHLGQVISRGERmEFTIQKSVELGVNVITPLWSERCGVKLDAERmDKKIQQWQKIAIAACEQCGRNIVPEIRPLmKLQDWCAENDGALKLNLHPRAHYSIKTLPTIPAGGVRLLIGSEGGLSAQEIAQTEQQGFTEILLGKRVLRTETASLAAISALQICFGDLGEA 246
                                    11        21        31  |     41        51        61        71        81        91|      101       111       121  |    131       141       151  |    161       171       181       191       201       211       221       231       241     
                                                           34-MSE                                                    92-MSE                         124-MSE                       154-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: All beta proteins (24004)

Fold: PUA domain-like (96)

Superfamily: PUA domain-like (96)

Family: YggJ N-terminal domain-like (6)

Protein domain: Hypothetical protein HI0303 (2)

Haemophilus influenzae [TaxId: 727] (2)

1a	d1nxza1	A:2-73
1b	d1nxzb1	B:2-73

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

Fold: alpha/beta knot (57)

Superfamily: alpha/beta knot (57)

Family: YggJ C-terminal domain-like (7)

Protein domain: Hypothetical protein HI0303 (2)

Haemophilus influenzae [TaxId: 727] (2)

2a	d1nxza2	A:74-247
2b	d1nxzb2	B:74-246

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)

Haemophilus influenzae. Organism_taxid: 727. (3)

1a	1nxzB02	B:74-246
1b	1nxzA02	A:74-247

Class: Mainly Beta (13760)

Architecture: Beta Barrel (4804)

Topology: Ribosomal Protein L25; Chain P (96)

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

Haemophilus influenzae. Organism_taxid: 727. (2)

2a	1nxzA01	A:2-73
2b	1nxzB01	B:2-73

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: SPOUT (28)

Family: Methyltrans_RNA (6)

Haemophilus influenzae (strain ATCC 51907 / DSM 11121 / KW20 / Rd) (2)

1a	Methyltrans_RNA-1nxzB01	B:18-238
1b	Methyltrans_RNA-1nxzB02	B:18-238

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (RSME_HAEIN | P44627)

molecular function
	GO:0008168	methyltransferase activity	Catalysis of the transfer of a methyl group to an acceptor molecule.
	GO:0070042	rRNA (uridine-N3-)-methyltransferase activity	Catalysis of the reaction: S-adenosyl-L-methionine + rRNA = S-adenosyl-L-homocysteine + rRNA containing N3-methyluridine.
	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: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
	Complete Structure
		Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
		WebMol \| AstexViewer[tm]@PDBe (Java Applets, require no local installation except for Java; loading may be slow)
		STRAP (Java WebStart application, automatic local installation, requires Java; full application with system access!)
		RasMol (require local installation)
		Molscript (VRML) (requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)

	Ligands, Modified Residues, Ions
		MSE	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
(no "Sites" information available for 1nxz)

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

Jmol
	protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick [ Asym./Biol. Unit PNG format ](automatic orientation, automatically generated)
Molscript
	protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick [ mono PDF format \| stereo PDF format ](default orientation, automatically generated)

Access by PDB/NDB ID
	1nxz
		Family and Domain Information	:	ProDom \| SYSTERS
		General Structural Information	:	GlycoscienceDB \| MMDB \| NDB \| OCA \| PDB \| PDBe \| PDBj \| PDBsum \| PDBWiki \| PQS \| PROTEOPEDIA
		Orientation in Membranes	:	OPM
		Protein Surface	:	SURFACE
		Secondary Structure	:	DSSP (structure derived) \| HSSP (homology derived)
		Structural Genomics	:	GeneCensus
		Structural Neighbours	:	CE \| VAST
		Structure Classification	:	CATH \| Dali \| SCOP
		Validation and Original Data	:	BMRB Data View \| BMRB Restraints Grid \| EDS \| PROCHECK \| RECOORD \| WHAT_CHECK

Access by UniProt ID/Accession number
	RSME_HAEIN \| P44627
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/SwissProt

Access by Enzyme Classificator (EC Number)
	(no 'Enzyme Classificator' available)
		General Enzyme Information	:	BRENDA \| EC-PDB \| Enzyme \| IntEnz
		Pathway	:	KEGG \| MetaCyc

Access by Disease Identifier (MIM ID)
	(no 'MIM ID' available)
		Disease Information	:	OMIM

Access by GenAge ID
	(no 'GenAge ID' available)
		Age Related Information	:	GenAge

Access by PDB/NDB ID
		Domain Information	:	XDom
		Interatomic Contacts of Structural Units	:	CSU
		Ligand-protein Contacts	:	LPC
		Protein Cavities	:	castP
		Sequence and Secondary Structure	:	PDBCartoon
		Structure Alignment	:	STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
		Structure and Sequence Browser	:	STING

Access by UniProt ID/Accession number
	RSME_HAEIN \| P44627
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

UniProtKB/Swiss-Prot
	RSME_HAEIN \| P44627	:	1vhy

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 8)

Sites (0, 0)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (2, 4)

CATH Domains (2, 4)

Pfam Domains (1, 2)

Gene Ontology (7, 7)

Visualization

Interactive Views

Still Images

Databases and Analysis Tools

Databases

Analysis Tools

Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File