Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym./Biol. Unit
collapse expand < >
Image Asym./Biol. Unit
Asym./Biol. Unit  (Jmol Viewer)

(-) Description

Title :  X-RAY CRYSTAL STRUCTURE OF PROTEIN NE0264 FROM NITROSOMONAS EUROPAEA. NORTHEAST STRUCTURAL GENOMICS CONSORTIUM TARGET NER5.
 
Authors :  F. Forouhar, M. Abashidze, S. M. Vorobiev, M. Ciano, L. -C. Ma, R. Shastr T. B. Acton, G. T. Montelione, L. Tong, J. F. Hunt, Northeast Structur Genomics Consortium (Nesg)
Date :  15 Sep 04  (Deposition) - 28 Sep 04  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.70
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Structural Genomics, Protein Structure Initiative, Nesg, Alpha-Beta Protein, Psi, Northeast Structural Genomics Consortium, Unknown Function (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  F. Forouhar, M. Abashidze, S. M. Vorobiev, M. Ciano, L. -C. Ma, R. Shastry, T. B. Acton, G. T. Montelione, L. Tong, J. F. Hunt
Crystal Structure Of The Hypothetical Protein From Nitrosomonas Europaea, Nesg Target Ner5
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - CONSERVED HYPOTHETICAL PROTEIN
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: BL21
    Expression System Strain: BL21(DE3)+MAGIC
    Expression System Taxid: 562
    Expression System Vector: PET21
    Expression System Vector Type: PLASMID
    Organism Scientific: NITROSOMONAS EUROPAEA
    Organism Taxid: 228410
    Strain: ATCC 19718
    Synonym: NC_840354

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 10)

Asymmetric/Biological Unit (1, 10)
No.NameCountTypeFull Name
1MSE10Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (0, 0)

(no "Site" information available for 1XFS)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Lys A:42 -Pro A:43
2Lys B:42 -Pro B:43

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1XFS)

(-) Sequences/Alignments

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:154
 aligned with Q82XK1_NITEU | Q82XK1 from UniProtKB/TrEMBL  Length:170

    Alignment length:165
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165     
         Q82XK1_NITEU     6 IDAELDLMLKRELAVPVNLVWRGLTEPELLKKWFVPKPWSISDCRVDLRPGGEFYTVMQDPEGNKFPNSGCFLEVTDEKRLIWTSALVKNYRPAVPATTSDKECAHIVMTAVIELQPTSSGTRYTACAMHNTPGQRKLHEEMGFHEGWGTTITQLEELLKQEKAY 170
               SCOP domains d1xfsa_ A: Hypothetical protein NE0264                                                                                                                                SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeeeeee..hhhhhhhhhhhhhhhh........eeeeeee......eeeeeee.....eeeeeeeeeeee...eeeee..eehhhee...-----------..eeeeeeee....eeeeeeee..hhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1xfs A   6 IDAELDLmLKRELAVPVNLVWRGLTEPELLKKWFVPKPWSISDCRVDLRPGGEFYTVmQDPEGNKFPNSGCFLEVTDEKRLIWTSALVKNYRPAVP-----------VmTAVIELQPTSSGTRYTACAmHNTPGQRKLHEEmGFHEGWGTTITQLEELLKQEKAY 170
                                   |15        25        35        45        55       |65        75        85        95     |   -       115       125       135       145 |     155       165     
                                  13-MSE                                            63-MSE                               101         113|                 134-MSE      147-MSE                   
                                                                                                                                      114-MSE                                                    


Chain B from PDB  Type:PROTEIN  Length:154
 aligned with Q82XK1_NITEU | Q82XK1 from UniProtKB/TrEMBL  Length:170

    Alignment length:165
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163     
         Q82XK1_NITEU     4 TPIDAELDLMLKRELAVPVNLVWRGLTEPELLKKWFVPKPWSISDCRVDLRPGGEFYTVMQDPEGNKFPNSGCFLEVTDEKRLIWTSALVKNYRPAVPATTSDKECAHIVMTAVIELQPTSSGTRYTACAMHNTPGQRKLHEEMGFHEGWGTTITQLEELLKQEK 168
               SCOP domains d1xfsb_ B: Hypothetical protein NE0264                                                                                                                                SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeeeeee..hhhhhhhhhhhhhhhh........eeeeeee......eeeeeee.....eeeeeeeeeeee...eeeee..eehhhee...----------...eeeeeeee....eeeeeeee..hhhhhhhhhhhhhh-hhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1xfs B   4 TPIDAELDLmLKRELAVPVNLVWRGLTEPELLKKWFVPKPWSISDCRVDLRPGGEFYTVmQDPEGNKFPNSGCFLEVTDEKRLIWTSALVKNYRPAVP----------IVmTAVIELQPTSSGTRYTACAmHNTPGQRKLHEEmGFH-GWGTTITQLEELLKQEK 168
                                    13        23        33        43        53        63        73        83        93       | -       113|      123       133|      143   |  |153       163     
                                    13-MSE                                            63-MSE                               101        112 |                 134-MSE      147-MSE|                
                                                                                                                                        114-MSE                             150 |                
                                                                                                                                                                              152
   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 '|'

 Classification and Annotation

(-) SCOP Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1XFS)

(-) Gene Ontology  (1, 1)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (Q82XK1_NITEU | Q82XK1)
biological process
    GO:0006950    response to stress    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a disturbance in organismal or cellular homeostasis, usually, but not necessarily, exogenous (e.g. temperature, humidity, ionizing radiation).

 Visualization

(-) Interactive Views

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 1xfs)
 
  Cis Peptide Bonds
    Lys A:42 - Pro A:43   [ RasMol ]  
    Lys B:42 - Pro B:43   [ RasMol ]  
 

(-) Still Images

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)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  1xfs
    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
  Q82XK1_NITEU | Q82XK1
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/TrEMBL
 
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

(-) Analysis Tools

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
  Q82XK1_NITEU | Q82XK1
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

(no "Entries Sharing at Least One Protein Chain" available for 1XFS)

(-) Related Entries Specified in the PDB File

ner5