Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Biol.Unit 1 - manually
(-)Asymmetric Unit
(-)Biological Unit 1
(-)Biological Unit 2
collapse expand < >
Image Biol.Unit 1 - manually
Biol.Unit 1 - manually  (Jmol Viewer)
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 :  ALANINE 31 PROLINE MUTANT OF ROP PROTEIN, MONOCLINIC FORM
 
Authors :  N. M. Glykos, M. Kokkinidis
Date :  13 Sep 01  (Deposition) - 12 Sep 02  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (2x)
Biol. Unit 2:  B  (2x)
Keywords :  Transcription Regulation (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  N. M. Glykos, M. Kokkinidis
Structure Determination Of A Small Protein Through A 23-Dimensional Molecular-Replacement Search.
Acta Crystallogr. , Sect. D V. 59 709 2003
PubMed-ID: 12657790  |  Reference-DOI: 10.1107/S0907444903002889
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - REGULATORY PROTEIN ROP
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PEX43
    Expression System Taxid: 562
    Mutation: YES
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562
    Strain: 71/72 (71/18 PLUS PCI857)URCE 8
    Synonym: RNA ONE MODULATOR, ROM

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 1GMG)

(-) Sites  (0, 0)

(no "Site" information available for 1GMG)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1GMG)

(-) 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:56
 aligned with ROP_ECOLX | P03051 from UniProtKB/Swiss-Prot  Length:63

    Alignment length:56
                                    10        20        30        40        50      
             ROP_ECOLX    1 MTKQEKTALNMARFIRSQTLTLLEKLNELDADEQADICESLHDHADELYRSCLARF 56
               SCOP domains d1gmga_ A: ROP protein                                   SCOP domains
               CATH domains 1gmgA00 A:1-56  [code=1.10.287.230, no name defined]     CATH domains
               Pfam domains -------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------- Transcript
                  1gmg A  1 MTKQEKTALNMARFIRSQTLTLLEKLNELDPDEQADICESLHDHADELYRSCLARF 56
                                    10        20        30        40        50      


Chain B from PDB  Type:PROTEIN  Length:54
 aligned with ROP_ECOLX | P03051 from UniProtKB/Swiss-Prot  Length:63

    Alignment length:54
                                    12        22        32        42        52    
             ROP_ECOLX    3 KQEKTALNMARFIRSQTLTLLEKLNELDADEQADICESLHDHADELYRSCLARF 56
               SCOP domains d1gmgb_ B: ROP protein                                 SCOP domains
               CATH domains 1gmgB00 B:3-56  [code=1.10.287.230, no name defined]   CATH domains
               Pfam domains ------------------------------------------------------ Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------ Transcript
                  1gmg B  3 KQEKTALNMARFIRSQTLTLLEKLNELDPDEQADICESLHDHADELYRSCLARF 56
                                    12        22        32        42        52
   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  (1, 2)

Asymmetric Unit
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (2, 2)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (ROP_ECOLX | P03051)
biological process
    GO:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0006351    transcription, DNA-templated    The cellular synthesis of RNA on a template of DNA.

 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
(no "Ligands, Modified Residues, Ions" information available for 1gmg)
 
  Sites
(no "Sites" information available for 1gmg)
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1gmg)
 
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
  1gmg
    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
  ROP_ECOLX | P03051
    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
  ROP_ECOLX | P03051
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        ROP_ECOLX | P03051: 1b6q 1f4m 1f4n 1gto 1nkd 1qx8 1rop 1rpo 1rpr 1yo7 2ghy 2ijh 2iji 2ijj 2ijk 3k79 4do2

(-) Related Entries Specified in the PDB File

1b6q ALANINE 31 PROLINE MUTANT OF ROP PROTEIN
1f4m P3(2) CRYSTAL STRUCTURE OF ALA2ILE2-6, A VERSION OF ROP WITH A REPACKED HYDROPHOBIC CORE AND A NEW FOLD.
1f4n C2 CRYSTAL STRUCTURE OF ALA2ILE2-6, A VERSION OF ROP WITH A REPACKED HYDROPHOBIC CORE AND A NEW FOLD.
1gto HIGH RESOLUTION STRUCTURE OF A HYPERSTABLE HELICAL BUNDLEPROTEIN MUTANT
1nkd ATOMIC RESOLUTION (1.07 ANGSTROMS) STRUCTURE OF THE ROP MUTANT <2AA>
1rop ROP: COLE1 REPRESSOR OF PRIMER
1rpo ROP (COLE1 REPRESSOR OF PRIMER) MUTANT WITH ALA INSERTED ON EITHER SIDE OF ASP 31 ( INS (A-D31-A))
1rpr ROP (REPRESSOR OF PRIMER) (NMR, 10 STRUCTURES)