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

(-) Description

Title :  THE CRYSTAL STRUCTURE OF A RRNA METHYLASE FROM STREPTOCOCCUS THERMOPHILUS TO 1.95A
 
Authors :  A. J. Stein, R. Mulligan, L. Freeman, A. Joachimiak, Midwest Center F Structural Genomics (Mcsg)
Date :  30 Apr 10  (Deposition) - 12 May 10  (Release) - 12 May 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.95
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Sam-Dependent, Psi, Mcsg, Structural Genomics, Midwest Center For Structural Genomics, Protein Structure Initiative, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. J. Stein, R. Mulligan, L. Freeman, A. Joachimiak
The Crystal Structure Of A Rrna Methylase From Streptococcus Thermophilus To 1. 95A
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - RRNA METHYLASE
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PMCSG7
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: STU1645
    Organism Scientific: STREPTOCOCCUS THERMOPHILUS
    Organism Taxid: 264199
    Strain: LMG 18311
    Synonym: SAM-DEPENDENT METHYLTRANSFERASE SUPERFAMILY

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (1, 14)
No.NameCountTypeFull Name
1MSE14Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (0, 0)

(no "Site" information available for 3MTI)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3MTI)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3MTI)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3MTI)

(-) 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:166
 aligned with Q5M2Z6_STRT2 | Q5M2Z6 from UniProtKB/TrEMBL  Length:182

    Alignment length:183
                             1                                                                                                                                                                                     
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179   
         Q5M2Z6_STRT2     - -MIKRPIHMSHDFLAEVLDDESIVVDATMGNGNDTAFLAGLSKKVYAFDVQEQALGKTSQRLSDLGIENTELILDGHENLDHYVREPIRAAIFNLGYLPSADKSVITKPHTTLEAIEKILDRLEVGGRLAIMIYYGHDGGDMEKDAVLEYVIGLDQRVFTAMLYQPLNQINTPPFLVMLEKLQ 182
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhh......eeee.....hhhhhhhhh...eeeeee.hhhhhhhhhhhhhhhh...eeeee.hhhhhhhh....eeeeeeee.-----------hhhhhhhhhhhhhhheeeeeeeeeee.------hhhhhhhhhhhhhh....eeeeeeee........eeeeeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3mti A   0 AmIKRPIHmSHDFLAEVLDDESIVVDATmGNGNDTAFLAGLSKKVYAFDVQEQALGKTSQRLSDLGIENTELILDGHENLDHYVREPIRAAIFNLG-----------KPHTTLEAIEKILDRLEVGGRLAImIY------DmEKDAVLEYVIGLDQRVFTAmLYQPLNQINTPPFLVmLEKLQ 182
                             |      |9        19        29        39        49        59        69        79        89     |   -       109       119       129 | |     -||     149       159 |     169       179   
                             |      8-MSE              28-MSE                                                             95         107                     131-MSE  140|                 161-MSE         177-MSE 
                             1-MSE                                                                                                                             133     141-MSE                                     


Chain B from PDB  Type:PROTEIN  Length:180
 aligned with Q5M2Z6_STRT2 | Q5M2Z6 from UniProtKB/TrEMBL  Length:182

    Alignment length:183
                             1                                                                                                                                                                                     
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179   
         Q5M2Z6_STRT2     - -MIKRPIHMSHDFLAEVLDDESIVVDATMGNGNDTAFLAGLSKKVYAFDVQEQALGKTSQRLSDLGIENTELILDGHENLDHYVREPIRAAIFNLGYLPSADKSVITKPHTTLEAIEKILDRLEVGGRLAIMIYYGHDGGDMEKDAVLEYVIGLDQRVFTAMLYQPLNQINTPPFLVMLEKLQ 182
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -------------------------------------------rRNA_methylase-3mtiB01 B:43-180                                                                                                           -- Pfam domains (1)
           Pfam domains (2) -------------------------------------------rRNA_methylase-3mtiB02 B:43-180                                                                                                           -- Pfam domains (2)
         Sec.struct. author ....hhhhhhhhhhhh......eeee.....hhhhhhhhh...eeeeee.hhhhhhhhhhhhhhhh...eeeee.hhhhhhhhh...eeeeeeee.........---..hhhhhhhhhhhhheeeeeeeeeee.......hhhhhhhhhhhhh.....eeeeeeee........eeeeeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3mti B   0 AmIKRPIHmSHDFLAEVLDDESIVVDATmGNGNDTAFLAGLSKKVYAFDVQEQALGKTSQRLSDLGIENTELILDGHENLDHYVREPIRAAIFNLGYLPSADKS---KPHTTLEAIEKILDRLEVGGRLAImIYYGHDGGDmEKDAVLEYVIGLDQRVFTAmLYQPLNQINTPPFLVmLEKLQ 182
                             |      |9        19        29        39        49        59        69        79        89        99   |   109       119       129 |     139 |     149       159 |     169       179   
                             1-MSE  8-MSE              28-MSE                                                                    103 107                     131-MSE   141-MSE             161-MSE         177-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  (0, 0)

(no "SCOP Domain" information available for 3MTI)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Clan: NADP_Rossmann (1239)

(-) Gene Ontology  (3, 3)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (Q5M2Z6_STRT2 | Q5M2Z6)
molecular function
    GO:0008168    methyltransferase activity    Catalysis of the transfer of a methyl group to an acceptor molecule.
    GO:0016740    transferase activity    Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
biological process
    GO:0032259    methylation    The process in which a methyl group is covalently attached to a molecule.

 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
    MSE  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
(no "Sites" information available for 3mti)
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 3mti)
 

(-) 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 ](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
  3mti
    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
  Q5M2Z6_STRT2 | Q5M2Z6
    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
  Q5M2Z6_STRT2 | Q5M2Z6
    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 3MTI)

(-) Related Entries Specified in the PDB File

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