Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asymmetric Unit
(-)Biological Unit 1
(-)Biological Unit 2
collapse expand < >
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)
Image Biological Unit 2
Biological Unit 2  (Jmol Viewer)

(-) Description

Title :  X-RAY CRYSTAL STRUCTURE OF PROTEIN SO4414 FROM SHEWANELLA ONEIDENSIS. NORTHEAST STRUCTURAL GENOMICS CONSORTIUM TARGET SOR52.
 
Authors :  F. Forouhar, M. Abashidze, S. M. Vorobiev, K. Conover, T. B. Acton, G. T. Montelione, J. F. Hunt, L. Tong, Northeast Structural Genomic Consortium (Nesg)
Date :  18 Apr 05  (Deposition) - 03 May 05  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.31
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  A,B  (2x)
Keywords :  All Alpha-Protein. , Structural Genomics, Psi, Protein Structure Initiative, Northeast Structural Genomics Consortium, Nesg, Unknown Function (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  F. Forouhar, M. Abashidze, S. M. Vorobiev, K. Conover, T. B. Acton, G. T. Montelione, J. F. Hunt, L. Tong
Crystal Structure Of The Hypothetical Protein So4414 From Shewanella Oneidensis, Nesg Target Sor52
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - HYPOTHETICAL PROTEIN SO4414
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET21
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Organism Scientific: SHEWANELLA ONEIDENSIS
    Organism Taxid: 211586
    Strain: MR-1

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): AB
Biological Unit 2 (2x): AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 14)

Asymmetric Unit (1, 14)
No.NameCountTypeFull Name
1MSE14Mod. Amino AcidSELENOMETHIONINE
Biological Unit 1 (1, 14)
No.NameCountTypeFull Name
1MSE14Mod. Amino AcidSELENOMETHIONINE
Biological Unit 2 (1, 28)
No.NameCountTypeFull Name
1MSE28Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (0, 0)

(no "Site" information available for 1ZEE)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1ZEE)

(-) Sequences/Alignments

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:363
 aligned with Q8E972_SHEON | Q8E972 from UniProtKB/TrEMBL  Length:392

    Alignment length:387
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       
         Q8E972_SHEON     6 YNTEAFDEWIRSRFVELNSQLEQLYYQQTDRANVQEVGTELKHTLESEGRELVKALLDEGNTDEGFDSAFDLLGNVGLYMAACRRHEITEPTRETTSPLLEASALAMHIGASIGVTPRFATAHLTTHNRAHNGIYKRFTDLPDEKLFVDYNTKGILAYKRASDALLKIQPLGISHPISHDLLRVTKQALQDVIESNQQLFNRLDTDRFFYCVRPYYKPYRVGSVVYRGANAGDFAGINVIDLTLGLCFANEASYSQMLVDKFLYMMPEDQQILRECMRRPNLMDDFLQAKGCIHQDWYQENLKLFIEVCELHGQTAIQHHNELVTKYIAEPSVSMEQQHLAKVTASGPPLHVLLASLERLRDRRAAVLRDDIRTRYYDLKKLKDSLR 392
               SCOP domains d1zeea1 A:6-392 Hypothetical protein SO4414                                                                                                                                                                                                                                                                                                                                                         SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhh............hhhhhhhhhhhhhhhh.....hhhhhh....ee..ee.....hhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhh.eee..eee.......hhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...------------------------.hhhhhhhhhhhhh.........hhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1zee A   6 YNTEAFDEWIRSRFVELNSQLEQLYYQQTDRANVQEVGTELKHTLESEGRELVKALLDEGNTDEGFDSAFDLLGNVGLYmAACRRHEITEPTRETTSPLLEASALAmHIGASIGVTPRFATAHLTTHNRAHNGIYKRFTDLPDEKLFVDYNTKGILAYKRASDALLKIQPLGISHPISHDLLRVTKQALQDVIESNQQLFNRLDTDRFFYCVRPYYKPYRVGSVVYRGANAGDFAGINVIDLTLGLCFANEASYSQmLVDKFLYmmPEDQQILRECmRRPNLmDDFLQAKGCIHQDWYQENLKLFIEVCELHGQTAIQHHNELVTKY------------------------VLLASLERLRDRRAAVLRDDIRTRYYDLKKLKDSLR 392
                                    15        25        35        45        55        65        75        85        95       105      |115       125       135       145       155       165       175       185       195       205       215       225       235       245       255      |265    || 275      |285  |    295       305       315       325      |  -         -         - |     365       375       385       
                                                                                                          85-MSE                    112-MSE                                                                                                                                               262-MSE 270-MSE     282-MSE |                                         332                      357                                   
                                                                                                                                                                                                                                                                                                   271-MSE          288-MSE                                                                                                    


Chain B from PDB  Type:PROTEIN  Length:363
 aligned with Q8E972_SHEON | Q8E972 from UniProtKB/TrEMBL  Length:392

    Alignment length:387
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       
         Q8E972_SHEON     6 YNTEAFDEWIRSRFVELNSQLEQLYYQQTDRANVQEVGTELKHTLESEGRELVKALLDEGNTDEGFDSAFDLLGNVGLYMAACRRHEITEPTRETTSPLLEASALAMHIGASIGVTPRFATAHLTTHNRAHNGIYKRFTDLPDEKLFVDYNTKGILAYKRASDALLKIQPLGISHPISHDLLRVTKQALQDVIESNQQLFNRLDTDRFFYCVRPYYKPYRVGSVVYRGANAGDFAGINVIDLTLGLCFANEASYSQMLVDKFLYMMPEDQQILRECMRRPNLMDDFLQAKGCIHQDWYQENLKLFIEVCELHGQTAIQHHNELVTKYIAEPSVSMEQQHLAKVTASGPPLHVLLASLERLRDRRAAVLRDDIRTRYYDLKKLKDSLR 392
               SCOP domains d1zeeb_ B: Hypothetical protein SO4414                                                                                                                                                                                                                                                                                                                                                              SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) DUF1864-1zeeB01 B:6-391                                                                                                                                                                                                                                                                                                                                                                           - Pfam domains (1)
           Pfam domains (2) DUF1864-1zeeB02 B:6-391                                                                                                                                                                                                                                                                                                                                                                           - Pfam domains (2)
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhh............hhhhhhhhhhhhhhhh.....hhhhhh....ee..ee.....hhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhh.eee..eee.......hhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...------------------------.hhhhhhhhhhhhhh........hhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1zee B   6 YNTEAFDEWIRSRFVELNSQLEQLYYQQTDRANVQEVGTELKHTLESEGRELVKALLDEGNTDEGFDSAFDLLGNVGLYmAACRRHEITEPTRETTSPLLEASALAmHIGASIGVTPRFATAHLTTHNRAHNGIYKRFTDLPDEKLFVDYNTKGILAYKRASDALLKIQPLGISHPISHDLLRVTKQALQDVIESNQQLFNRLDTDRFFYCVRPYYKPYRVGSVVYRGANAGDFAGINVIDLTLGLCFANEASYSQmLVDKFLYmmPEDQQILRECmRRPNLmDDFLQAKGCIHQDWYQENLKLFIEVCELHGQTAIQHHNELVTKY------------------------VLLASLERLRDRRAAVLRDDIRTRYYDLKKLKDSLR 392
                                    15        25        35        45        55        65        75        85        95       105      |115       125       135       145       155       165       175       185       195       205       215       225       235       245       255      |265    || 275      |285  |    295       305       315       325      |  -         -         - |     365       375       385       
                                                                                                          85-MSE                    112-MSE                                                                                                                                               262-MSE 270-MSE     282-MSE |                                         332                      357                                   
                                                                                                                                                                                                                                                                                                   271-MSE          288-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 '|'

 Classification and Annotation

(-) SCOP Domains  (1, 2)

Asymmetric Unit
(-)
Class: All alpha proteins (14657)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Clan: IDO-like (6)

(-) Gene Ontology  (7, 7)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (Q8E972_SHEON | Q8E972)
molecular function
    GO:0051213    dioxygenase activity    Catalysis of an oxidation-reduction (redox) reaction in which both atoms of oxygen from one molecule of O2 are incorporated into the (reduced) product(s) of the reaction. The two atoms of oxygen may be distributed between two different products.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0003674    molecular_function    Elemental activities, such as catalysis or binding, describing the actions of a gene product at the molecular level. A given gene product may exhibit one or more molecular functions.
    GO:0016491    oxidoreductase activity    Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
    GO:0004833    tryptophan 2,3-dioxygenase activity    Catalysis of the reaction: L-tryptophan + O2 = N-formyl-L-kynurenine.
biological process
    GO:0008150    biological_process    Any process specifically pertinent to the functioning of integrated living units: cells, tissues, organs, and organisms. A process is a collection of molecular events with a defined beginning and end.
    GO:0055114    oxidation-reduction process    A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.

 Visualization

(-) Interactive Views

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 1zee)
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1zee)
 
Biological Units
  Complete Structure
    Biological Unit 1  [ Jena3D ]
    Biological Unit 2  [ Jena3D ]

(-) Still Images

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 ](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
  1zee
    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
  Q8E972_SHEON | Q8E972
    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
  Q8E972_SHEON | Q8E972
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/TrEMBL
        Q8E972_SHEON | Q8E972: 2nwb

(-) Related Entries Specified in the PDB File

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