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

(-) Description

Title :  CRYSTAL STRUCTURE OF ISCA WITH THE [2FE-2S] CLUSTER
 
Authors :  K. Morimoto, E. Yamashita, Y. Kondou, S. J. Lee, T. Tsukihara, M. Nakai
Date :  22 Mar 05  (Deposition) - 06 Jun 06  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  [2Fe-2S], Biosynthesis, Cyanobacteria, Domain Swapping, Fe- S Cluster, Iron, Iron-Sulfur Cluster Protein, Isc, Isca, Scaffold, Sulfur, Tetrameric, Three Conserved Cys, Metal Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. Morimoto, E. Yamashita, Y. Kondou, S. J. Lee, F. Arisaka, T. Tsukihara, M. Nakai
The Asymmetric Isca Homodimer With An Exposed [2Fe-2S] Cluster Suggests The Structural Basis Of The Fe-S Cluster Biosynthetic Scaffold.
J. Mol. Biol. V. 360 117 2006
PubMed-ID: 16730357  |  Reference-DOI: 10.1016/J.JMB.2006.04.067
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - ISCA
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET21B
    Expression System Strain: BL-21(DE3)RIL
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: TLL0464
    Organism Scientific: THERMOSYNECHOCOCCUS ELONGATUS
    Organism Taxid: 197221
    Strain: BP-1
    Synonym: HYPOTHETICAL PROTEIN TLL0464

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

Asymmetric/Biological Unit (2, 4)
No.NameCountTypeFull Name
1FES2Ligand/IonFE2/S2 (INORGANIC) CLUSTER
2NA2Ligand/IonSODIUM ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER B:35 , GLU B:36 , CYS B:37 , SER C:35 , GLU C:36 , GLY C:38 , HOH D:116BINDING SITE FOR RESIDUE NA C 1001
2AC2SOFTWARESER A:35 , GLU A:36 , GLY A:38 , SER D:35 , GLU D:36 , HOH D:120BINDING SITE FOR RESIDUE NA A 1002
3AC3SOFTWARECYS A:37 , CYS A:101 , CYS A:103 , CYS D:103BINDING SITE FOR RESIDUE FES A 500
4AC4SOFTWARECYS B:103 , GLY B:104 , CYS C:37 , CYS C:101 , CYS C:103BINDING SITE FOR RESIDUE FES C 1500

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1X0G)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1X0G)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1X0G)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1X0G)

(-) Exons   (0, 0)

(no "Exon" information available for 1X0G)

(-) 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:102
 aligned with Q8DLM0_THEEB | Q8DLM0 from UniProtKB/TrEMBL  Length:112

    Alignment length:112
                                    10        20        30        40        50        60        70        80        90       100       110  
         Q8DLM0_THEEB     1 MVELTPAAIQELERLQTHGVRRGQAAILRIQVQPSECGDWRYDLALVAEPKPTDLLTQSQGWTIAIAAEAAELLRGLRVDYIEDLMGGAFRFHNPNASQTCGCGMAFRVSRS 112
               SCOP domains d1x0ga_ A: autom          ated matches                                                                           SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eehhhhhhhh....----------.eeeeeee.....eeeeeee........eee......eee...hhhhhh..eeeeeee..eeeeeee.....ee.....eee.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------- Transcript
                 1x0g A   1 MVELTPAAIQELERLQ----------ILRIQVQPSECGDWRYDLALVAEPKPTDLLTQSQGWTIAIAAEAAELLRGLRVDYIEDLMGGAFRFHNPNASQTCGCGMAFRVSRS 112
                                    10     |   -      | 30        40        50        60        70        80        90       100       110  
                                          16         27                                                                                     


Chain B from PDB  Type:PROTEIN  Length:110
 aligned with Q8DLM0_THEEB | Q8DLM0 from UniProtKB/TrEMBL  Length:112

    Alignment length:110
                                    10        20        30        40        50        60        70        80        90       100       110
         Q8DLM0_THEEB     1 MVELTPAAIQELERLQTHGVRRGQAAILRIQVQPSECGDWRYDLALVAEPKPTDLLTQSQGWTIAIAAEAAELLRGLRVDYIEDLMGGAFRFHNPNASQTCGCGMAFRVS 110
               SCOP domains d1x0gb_ B: automated matches                                                                                   SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eehhhhhhhhhhhhh.........eeeeeeeeeeeeeeeeeeee........eeeee..eeeee...hhhhhh..eeeeeee..eeeeeee.hhh.eee......... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------- Transcript
                 1x0g B   1 MVELTPAAIQELERLQTHGVRRGQAAILRIQVQPSECGDWRYDLALVAEPKPTDLLTQSQGWTIAIAAEAAELLRGLRVDYIEDLMGGAFRFHNPNASQTCGCGMAFRVS 110
                                    10        20        30        40        50        60        70        80        90       100       110


Chain C from PDB  Type:PROTEIN  Length:111
 aligned with Q8DLM0_THEEB | Q8DLM0 from UniProtKB/TrEMBL  Length:112

    Alignment length:111
                                    10        20        30        40        50        60        70        80        90       100       110 
         Q8DLM0_THEEB     1 MVELTPAAIQELERLQTHGVRRGQAAILRIQVQPSECGDWRYDLALVAEPKPTDLLTQSQGWTIAIAAEAAELLRGLRVDYIEDLMGGAFRFHNPNASQTCGCGMAFRVSR 111
               SCOP domains d1x0gc_ C: automated matches                                                                                    SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eehhhhhhhhhhhh..........eeeeeeee.....eeeeeee........eeeee..eeeee...hhhhhh..eeeee......eeeee.....ee.....eee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------- Transcript
                 1x0g C   1 MVELTPAAIQELERLQTHGVRRGQAAILRIQVQPSECGDWRYDLALVAEPKPTDLLTQSQGWTIAIAAEAAELLRGLRVDYIEDLMGGAFRFHNPNASQTCGCGMAFRVSR 111
                                    10        20        30        40        50        60        70        80        90       100       110 


Chain D from PDB  Type:PROTEIN  Length:104
 aligned with Q8DLM0_THEEB | Q8DLM0 from UniProtKB/TrEMBL  Length:112

    Alignment length:110
                                    10        20        30        40        50        60        70        80        90       100       110
         Q8DLM0_THEEB     1 MVELTPAAIQELERLQTHGVRRGQAAILRIQVQPSECGDWRYDLALVAEPKPTDLLTQSQGWTIAIAAEAAELLRGLRVDYIEDLMGGAFRFHNPNASQTCGCGMAFRVS 110
               SCOP domains d1x0gd_ D: automat      ed matches                                                                             SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -Fe-S_biosyn-1x0gD      01 D:2-95                                                              --------------- Pfam domains (1)
           Pfam domains (2) -Fe-S_biosyn-1x0gD      02 D:2-95                                                              --------------- Pfam domains (2)
           Pfam domains (3) -Fe-S_biosyn-1x0gD      03 D:2-95                                                              --------------- Pfam domains (3)
           Pfam domains (4) -Fe-S_biosyn-1x0gD      04 D:2-95                                                              --------------- Pfam domains (4)
         Sec.struct. author ..eehhhhhhhhhhhhh.------...eeeeeeeeeeeeeeeeeeee.......eeeee..eeeee..hhhhhhh..eeeeeee..eeeeeee.....eee......... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------- Transcript
                 1x0g D   1 MVELTPAAIQELERLQTH------AAILRIQVQPSECGDWRYDLALVAEPKPTDLLTQSQGWTIAIAAEAAELLRGLRVDYIEDLMGGAFRFHNPNASQTCGCGMAFRVS 110
                                    10       | -    |   30        40        50        60        70        80        90       100       110
                                            18     25
   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, 4)

Asymmetric/Biological Unit
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1X0G)

(-) Pfam Domains  (1, 4)

Asymmetric/Biological Unit
(-)
Clan: no clan defined [family: Fe-S_biosyn] (4)

(-) Gene Ontology  (5, 5)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C,D   (Q8DLM0_THEEB | Q8DLM0)
molecular function
    GO:0051537    2 iron, 2 sulfur cluster binding    Interacting selectively and non-covalently with a 2 iron, 2 sulfur (2Fe-2S) cluster; this cluster consists of two iron atoms, with two inorganic sulfur atoms found between the irons and acting as bridging ligands.
    GO:0051536    iron-sulfur cluster binding    Interacting selectively and non-covalently with an iron-sulfur cluster, a combination of iron and sulfur atoms.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0005198    structural molecule activity    The action of a molecule that contributes to the structural integrity of a complex or its assembly within or outside a cell.
biological process
    GO:0016226    iron-sulfur cluster assembly    The incorporation of iron and exogenous sulfur into a metallo-sulfur cluster.

 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
    FES  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    NA  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1x0g)
 

(-) 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 | Asym./Biol. Unit - sites 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
  1x0g
    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
  Q8DLM0_THEEB | Q8DLM0
    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
  Q8DLM0_THEEB | Q8DLM0
    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 1X0G)

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1X0G)