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 THE PHOSPHORYLATED CYANOBACTERIAL PHYTOCHROME RESPONSE REGULATOR RCPA
 
Authors :  C. Benda, C. Scheufler, N. Tandeau De Marsac, W. Gaertner
Date :  15 Oct 01  (Deposition) - 16 Dec 03  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Phosphorylated Aspartate, Response Regulator, Chey Homologue, Homodimer, (Beta/Alpha)5, Signaling Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. Benda, C. Scheufler, N. Tandeau De Marsac, W. Gaertner
Crystal Structures Of Two Cyanobacterial Response Regulators In Apo- And Phosphorylated Form Reveal A Novel Dimerization Motif Of Phytochrome-Associated Response Regulators
Biophys. J. V. 87 476 2004
PubMed-ID: 15240481  |  Reference-DOI: 10.1529/BIOPHYSJ.103.033696
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PHYTOCHROME RESPONSE REGULATOR RCPA
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28A(+)
    Expression System Strain: BL21 (DE3) GOLD, NOVAGEN
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: AF309559
    Organism Scientific: TOLYPOTHRIX SP. PCC 7601
    Organism Taxid: 1188

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (2, 4)
No.NameCountTypeFull Name
1MG2Ligand/IonMAGNESIUM ION
2PHD2Mod. Amino AcidASPARTYL PHOSPHATE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:17 , ASP A:18 , PHD A:70 , ASN A:72 , HOH A:507 , HOH A:553BINDING SITE FOR RESIDUE MG A 501
2AC2SOFTWAREASP B:18 , PHD B:70 , ASN B:72BINDING SITE FOR RESIDUE MG B 502

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1K68)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1K68)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1K68)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1K68)

(-) Exons   (0, 0)

(no "Exon" information available for 1K68)

(-) 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:140
 aligned with Q8RTN0_9CYAN | Q8RTN0 from UniProtKB/TrEMBL  Length:148

    Alignment length:140
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147
         Q8RTN0_9CYAN     8 KHKKIFLVEDNKADIRLIQEALKNSTVPHEVVTVRDGMEAMAYLRQEGEYANASRPDLILLDLNLPKKDGREVLAEIKSDPTLKRIPVVVLTTSRNEDDIFHSYDLHVNCYITKSRNLSQLFQIVKGIEEFWLSTATLPS 147
               SCOP domains d1k68a_ A: Response regulator for cyanobacterial phytochrome                                                                                 SCOP domains
               CATH domains 1k68A00 A:9-148  [code=3.40.50.2300, no name defined]                                                                                        CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee..hhhhhhhhhhhhhh.....eeeee.hhhhhhhhhh.hhhhhh.....eeee.......hhhhhhhhhhhh.hhhhh.eeeee...hhhhhhhhhhh...eeee...hhhhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1k68 A   9 AHKKIFLVEDNKADIRLIQEALANSTVPHEVVTVRDGMEAMAYLRQEGEYANASRPDLILLdLNLPKKDGREVLAEIKSDPTLKRIPVVVLSTSINEDDIFHSYDLHVNCYITKSANLSQLFQIVKGIEEFWLSTATLPS 148
                                    18        28        38        48        58        68 |      78        88        98       108       118       128       138       148
                                                                                        70-PHD                                                                          


Chain B from PDB  Type:PROTEIN  Length:140
 aligned with Q8RTN0_9CYAN | Q8RTN0 from UniProtKB/TrEMBL  Length:148

    Alignment length:140
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147
         Q8RTN0_9CYAN     8 KHKKIFLVEDNKADIRLIQEALKNSTVPHEVVTVRDGMEAMAYLRQEGEYANASRPDLILLDLNLPKKDGREVLAEIKSDPTLKRIPVVVLTTSRNEDDIFHSYDLHVNCYITKSRNLSQLFQIVKGIEEFWLSTATLPS 147
               SCOP domains d1k68b_ B: Response regulator for cyanobacterial phytochrome                                                                                 SCOP domains
               CATH domains 1k68B00 B:9-148  [code=3.40.50.2300, no name defined]                                                                                        CATH domains
           Pfam domains (1) ----Response_reg-1k68B01 B:13-134                                                                                             -------------- Pfam domains (1)
           Pfam domains (2) ----Response_reg-1k68B02 B:13-134                                                                                             -------------- Pfam domains (2)
         Sec.struct. author ...eeeee..hhhhhhhhhhhh.......eeeee.hhhhhhhhhh.hhhhh......eeee.......hhhhhhhhhhhh.......eeeee...hhhhhhhhhhh...eeee.....hhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1k68 B   9 AHKKIFLVEDNKADIRLIQEALANSTVPHEVVTVRDGMEAMAYLRQEGEYANASRPDLILLdLNLPKKDGREVLAEIKSDPTLKRIPVVVLSTSINEDDIFHSYDLHVNCYITKSANLSQLFQIVKGIEEFWLSTATLPS 148
                                    18        28        38        48        58        68 |      78        88        98       108       118       128       138       148
                                                                                        70-PHD
   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) (23833)

(-) CATH Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Clan: CheY (97)

(-) Gene Ontology  (3, 3)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (Q8RTN0_9CYAN | Q8RTN0)
molecular function
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
biological process
    GO:0000160    phosphorelay signal transduction system    A conserved series of molecular signals found in prokaryotes and eukaryotes; involves autophosphorylation of a histidine kinase and the transfer of the phosphate group to an aspartate that then acts as a phospho-donor to response regulator proteins.
cellular component
    GO:0005622    intracellular    The living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm.

 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
    MG  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    PHD  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1k68)
 

(-) 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
  1k68
    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
  Q8RTN0_9CYAN | Q8RTN0
    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
  Q8RTN0_9CYAN | Q8RTN0
    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 1K68)

(-) Related Entries Specified in the PDB File

1k66 APO-FORM OF A HOMOLOGUE RESPONSE REGULATOR FROM THE SAME ORGANISM