1VHY - JenaLib

Asymmetric Unit (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Biological Unit 3 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF HAEMOPHILUS INFLUENZAE PROTEIN HI0303, PFAM DUF558

Authors :   Structural Genomix, S. K. Burley, New York Sgx Research Center F Structural Genomics (Nysgxrc)

Date :   01 Dec 03 (Deposition) - 30 Dec 03 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.90

Chains :   Asym. Unit : A,B
Biol. Unit 1: A  (1x)
Biol. Unit 2: B  (1x)
Biol. Unit 3: A,B  (1x)

Keywords :   Psi, Protein Structure Initiative, New York Sgx Research Center For Structural Genomics, Nysgxrc, Structural Genomics, Unknown Function (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

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 Unit	:	A	B
Biological Unit 1 (1x)	:	A
Biological Unit 2 (1x)	:		B
Biological Unit 3 (1x)	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 8)

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

Biological Unit 1 (1, 4)

No.	Name	Count	Type	Full Name
1	MSE	4	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, 8)

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

(no "Site" information available for 1VHY)

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

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

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

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

(no "Exon" information available for 1VHY)

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:241
 aligned with RSME_HAEIN | P44627 from UniProtKB/Swiss-Prot  Length:245

    Alignment length:245
                                                                                                                                                                                                                                                                            245  
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242  |  
           RSME_HAEIN     3 IPRIYHPISLENQTQCYLSEDAANHVARVLRMTEGEQLELFDGSNHIYPAKIIESNKKSVKVEILGRELADKESHLKIHLGQVISRGERMEFTIQKSVELGVNVITPLWSERCGVKLDAERMDKKIQQWQKIAIAACEQCGRNIVPEIRPLMKLQDWCAENDGALKLNLHPRAHYSIKTLPTIPAGGVRLLIGSEGGLSAQEIAQTEQQGFTEILLGKRVLRTETASLAAISALQICFGDLGE--   -
               SCOP domains d1vhya1 A:3-73 Hypothetical protein HI0303                             d1vhya2 A:74-    247 Hypothetical protein HI0303                                                                                                                               SCOP domains
               CATH domains 1vhyA01 A:3-73 Hypothetical PUA domain-like; domain 1                  1vhyA02 A:74-    247  [code=3.40.1280.10, no name defined]                                                                                                                     CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eee.........eee.hhhhhhhhhh........eeeee....eeeeeeeeee....eeeee...ee........eeeeee.----.hhhhhhhhhhh...eeeeee........hhhhhhhhhhhhhhhhhhhhhhhh.....ee...eehhhhhh.....eeeee......hhhhh.......eeeee......hhhhhhhhhhh..eee.......hhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1vhy A   3 IPRIYHPISLENQTQCYLSEDAANHVARVLRmTEGEQLELFDGSNHIYPAKIIESNKKSVKVEILGRELADKESHLKIHLGQVI----RmEFTIQKSVELGVNVITPLWSERCGVKLDAERmDKKIQQWQKIAIAACEQCGRNIVPEIRPLmKLQDWCAENDGALKLNLHPRAHYSIKTLPTIPAGGVRLLIGSEGGLSAQEIAQTEQQGFTEILLGKRVLRTETASLAAISALQICFGDLGEEG 247
                                    12        22        32 |      42        52        62        72        82   |    92       102       112       122 |     132       142       152 |     162       172       182       192       202       212       222       232       242     
                                                          34-MSE                                              86   91|                             124-MSE                       154-MSE                                                                                         
                                                                                                                    92-MSE

Chain B from PDB  Type:PROTEIN  Length:237
 aligned with RSME_HAEIN | P44627 from UniProtKB/Swiss-Prot  Length:245

    Alignment length:245
                                                                                                                                                                                                                                                                            245  
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242  |  
           RSME_HAEIN     3 IPRIYHPISLENQTQCYLSEDAANHVARVLRMTEGEQLELFDGSNHIYPAKIIESNKKSVKVEILGRELADKESHLKIHLGQVISRGERMEFTIQKSVELGVNVITPLWSERCGVKLDAERMDKKIQQWQKIAIAACEQCGRNIVPEIRPLMKLQDWCAENDGALKLNLHPRAHYSIKTLPTIPAGGVRLLIGSEGGLSAQEIAQTEQQGFTEILLGKRVLRTETASLAAISALQICFGDLGE--   -
               SCOP domains d1vhyb1 B:3-73 Hypothetical protein HI0303                             d1vhyb2 B:74-24  7 Hypothetical protein HI0303                                                                                                                                 SCOP domains
               CATH domains 1vhyB01 B:3-73 Hypothetical PUA domain-like; domain 1                  1vhyB02 B:74-24  7  [code=3.40.1280.10, no name defined]                                                                                                                       CATH domains
           Pfam domains (1) ---------------Methyltrans_RNA-1vhyB01 B:18-238                                                                                                                                                                                             --------- Pfam domains (1)
           Pfam domains (2) ---------------Methyltrans_RNA-1vhyB02 B:18-238                                                                                                                                                                                             --------- Pfam domains (2)
         Sec.struct. author ..eee.........eee.hhhhhhhhh.........eeeee....eeeeee..------.eeee...ee........eeeeee...--hhhhhhhhhhhh...eeeeee............hhhhhhhhhhhhhhhhhhhh.....ee...eehhhhhh.....eeeee..................eeeee......hhhhhhhhhhh..eee.......hhhhhhhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1vhy B   3 IPRIYHPISLENQTQCYLSEDAANHVARVLRmTEGEQLELFDGSNHIYPAKII------VKVEILGRELADKESHLKIHLGQVISR--RmEFTIQKSVELGVNVITPLWSERCGVKLDAERmDKKIQQWQKIAIAACEQCGRNIVPEIRPLmKLQDWCAENDGALKLNLHPRAHYSIKTLPTIPAGGVRLLIGSEGGLSAQEIAQTEQQGFTEILLGKRVLRTETASLAAISALQICFGDLGEEG 247
                                    12        22        32 |      42        52  |     62        72        82     |  92       102       112       122 |     132       142       152 |     162       172       182       192       202       212       222       232       242     
                                                          34-MSE               55     62                        88 91|                             124-MSE                       154-MSE                                                                                         
                                                                                                                    92-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: 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	d1vhya1	A:3-73
1b	d1vhyb1	B:3-73

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	d1vhya2	A:74-247
2b	d1vhyb2	B:74-247

Asymmetric 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	1vhyA02	A:74-247
1b	1vhyB02	B: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	1vhyA01	A:3-73
2b	1vhyB01	B:3-73

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: SPOUT (28)

Family: Methyltrans_RNA (6)

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

1a	Methyltrans_RNA-1vhyB01	B:18-238
1b	Methyltrans_RNA-1vhyB02	B:18-238

Asymmetric 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 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 1vhy)

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

Biological Units
	Complete Structure
		Biological Unit 1	[ Jena3D ]
		Biological Unit 2	[ Jena3D ]
		Biological Unit 3	[ Jena3D ]

Jmol
	protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick [ Asym. Unit PNG format \| Biol. Unit 1 PNG format \| Biol. Unit 2 PNG format \| Biol. Unit 3 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
	1vhy
		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	:	1nxz

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