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 :  THE 1.7 ANGSTROM RESOLUTION CRYSTAL STRUCTURE OF AT2G44920, A PENTAPEPTIDE REPEAT PROTEIN FROM ARABIDOPSIS THALIANA THYLAKOID LUMEN.
 
Authors :  S. Ni, M. Mckgookey, S. L. Tinch, A. N. Jones, S. Jayaraman, M. A. Kennedy
Date :  28 May 10  (Deposition) - 29 Jun 11  (Release) - 29 Jun 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.70
Chains :  Asym./Biol. Unit :  A
Keywords :  Right-Handed Quadrilateral Beta Helix, Pentapeptide Repeat Protein, Repeated-Five Residue Fold, Chloroplast Lumen, Unknown Function (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Ni, M. Mckgookey, S. L. Tinch, A. N. Jones, S. Jayaraman, M. A. Kenned
The 1. 7 Angstrom Resolution Crystal Structure Of At2G44920, A Pentapeptide Repeat Protein From Arabidopsis Thaliana Thylakoid Lumen.
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - THYLAKOID LUMENAL 15 KDA PROTEIN 1, CHLOROPLASTIC
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28B
    Expression System Strain: BL21DE3
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 81-224
    Gene: AT2G44920, T13E15.7
    Mutation: YES
    Organism Common: MOUSE EAR CRESS
    Organism Scientific: ARABIDOPSIS THALIANA
    Organism Taxid: 3702
    Synonym: P15

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1SO41Ligand/IonSULFATE ION

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR A:88 , GLY A:89 , GLN A:90 , ARG A:110 , GLY A:130 , HOH A:237 , HOH A:282 , HOH A:288BINDING SITE FOR RESIDUE SO4 A 500

(-) SS Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1A:203 -A:223

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Gly A:86 -Pro A:87

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3N90)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3N90)

(-) Exons   (0, 0)

(no "Exon" information available for 3N90)

(-) 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:145
 aligned with TL15A_ARATH | O22160 from UniProtKB/Swiss-Prot  Length:224

    Alignment length:145
                                                                                                                                                                         224 
                                    90       100       110       120       130       140       150       160       170       180       190       200       210       220   | 
          TL15A_ARATH    81 AFKGGGPYGQGVTRGQDLSGKDFSGQTLIRQDFKTSILRQANFKGAKLLGASFFDADLTGADLSEADLRGADFSLANVTKVNLTNANLEGATVTGNTSFKGSNITGADFTDVPLRDDQRVYLCKVADGVNATTGNATRDTLLCN-   -
               SCOP domains d3n90a_ A: automated matches                                                                                                                      SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -------------------------------------------------------Pentapeptide-3n90A01 A:136-175          -------------------------------------------------- Pfam domains (1)
           Pfam domains (2) -------------------------------------------------------Pentapeptide-3n90A02 A:136-175          -------------------------------------------------- Pfam domains (2)
         Sec.struct. author hhhhhh..hhhhhh....................................................................................................hhhhhhhhhhhh.........hhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3n90 A  81 AFKGGGPYGQGVTRGQDLSGKDFSGQTLIRQDFKTSILRQANFKGAKLLGASFFDADLTGADLSEADLRGADFSLANVTKVNLTNANLEGATMMGNTSFKGSNITGADFTDVPLRDDQRVYLCKVADGVNATTGNATRDTLLCNL 225
                                    90       100       110       120       130       140       150       160       170       180       190       200       210       220
   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, 1)

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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3N90)

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Clan: Pentapeptide (11)

(-) Gene Ontology  (9, 9)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (TL15A_ARATH | O22160)
molecular function
    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:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
cellular component
    GO:0009507    chloroplast    A chlorophyll-containing plastid with thylakoids organized into grana and frets, or stroma thylakoids, and embedded in a stroma.
    GO:0009534    chloroplast thylakoid    Sac-like membranous structures (cisternae) in a chloroplast combined into stacks (grana) and present singly in the stroma (stroma thylakoids or frets) as interconnections between grana. An example of this component is found in Arabidopsis thaliana.
    GO:0009543    chloroplast thylakoid lumen    The cavity enclosed within the chloroplast thylakoid membrane. An example of this component is found in Arabidopsis thaliana.
    GO:0009535    chloroplast thylakoid membrane    The pigmented membrane of a chloroplast thylakoid. An example of this component is found in Arabidopsis thaliana.
    GO:0009536    plastid    Any member of a family of organelles found in the cytoplasm of plants and some protists, which are membrane-bounded and contain DNA. Plant plastids develop from a common type, the proplastid.
    GO:0009579    thylakoid    A membranous cellular structure that bears the photosynthetic pigments in plants, algae, and cyanobacteria. In cyanobacteria thylakoids are of various shapes and are attached to, or continuous with, the plasma membrane. In eukaryotes they are flattened, membrane-bounded disk-like structures located in the chloroplasts; in the chloroplasts of higher plants the thylakoids form dense stacks called grana. Isolated thylakoid preparations can carry out photosynthetic electron transport and the associated phosphorylation.
    GO:0031977    thylakoid lumen    The volume enclosed by a thylakoid membrane.

 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
    SO4  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Gly A:86 - Pro A:87   [ 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 | 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
  3n90
    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
  TL15A_ARATH | O22160
    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

(-) 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
  TL15A_ARATH | O22160
    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 3N90)

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 3N90)