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 PROBABLE RRNA-METHYLTRANSFERASE FROM PORPHYROMONAS GINGIVALIS
 
Authors :  U. A. Ramagopal, R. Toro, S. K. Burley, S. C. Almo, New York Sgx Research Center For Structural Genomics (Nysgxrc)
Date :  30 Nov 09  (Deposition) - 19 Jan 10  (Release) - 19 Jan 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Structural Genomics, Unknown Function, Psi-2, Protein Structure Initiative, New York Sgx Research Center For Structural Genomics, Nysgxrc (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  U. A. Ramagopal, R. Toro, S. K. Burley, S. C. Almo
Crystal Structure Of Probable Rrna-Methyltransferase From Porphyromonas Gingivalis
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PROBABLE R-RNA METHYLTRANSFERASE
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: BC-PSGX4(BC)
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Gene: PGN_0201
    Organism Scientific: PORPHYROMONAS GINGIVALIS ATCC 33277
    Organism Taxid: 431947
    Strain: ATCC 33277 /DSM 20709 /JCM 12257

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 10)

Asymmetric/Biological Unit (2, 10)
No.NameCountTypeFull Name
1ADN2Ligand/IonADENOSINE
2MSE8Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREALA A:164 , TYR A:165 , VAL A:166 , ARG A:178 , ILE A:195 , GLY A:196 , PRO A:197 , ASP A:200 , SER A:218 , LEU A:219 , GLY A:220 , SER A:222 , LEU A:224 , THR A:226 , ALA A:229BINDING SITE FOR RESIDUE ADN A 300
2AC2SOFTWAREALA B:164 , TYR B:165 , ARG B:178 , ILE B:195 , GLY B:196 , PRO B:197 , ASP B:200 , VAL B:217 , SER B:218 , LEU B:219 , GLY B:220 , LEU B:224 , THR B:226 , ALA B:229BINDING SITE FOR RESIDUE ADN B 300

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3KW2)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3KW2)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3KW2)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3KW2)

(-) Exons   (0, 0)

(no "Exon" information available for 3KW2)

(-) 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:240
 aligned with B2RH75_PORG3 | B2RH75 from UniProtKB/TrEMBL  Length:248

    Alignment length:245
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242     
         B2RH75_PORG3     3 LPLFYAPDIEQSDRLPDDEAGHILRVLRMQAGDRLRLTDGRGSFFDAVIETADRKSCYVSVCGQESWQKPWRDRITIAIAPTKQSERMEWMLEKLVEIGVDEVVFIESEHSERRRIKAERLERIAISAMKQSLKASFPVIRVNIPIQTVIADTPKAAVRLIAYVDEAVRAEITQGRGYPSDFYHVGQDVLILIGPEGDFSPSEVESALLAGFAPVSLGESRLRTETAGLVACQWIHTLQACYRIG 247
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eee..........hhhhhhhhhh........eeeee....eeeeeeeeee....eeeeeeeeee........eeeee....hhhhhhhhhhhhhhhh..eeeeee.........hhhhhhhhhhhhhhhh......eeeeeeehhhhhhhh....eeeee.......-----...hhhhh......eeeee......hhhhhhhhhhhh.eee.......hhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3kw2 A   3 LPLFYAPDIEQSDRLPDDEAGHILRVLRmQAGDRLRLTDGRGSFFDAVIETADRKSCYVSVCGQESWQKPWRDRITIAIAPTKQSERmEWmLEKLVEIGVDEVVFIESEHSERRRIKAERLERIAISAmKQSLKASFPVIRVNIPIQTVIADTPKAAVRLIAYVDEAVR-----GRGYPSDFYHVGQDVLILIGPEGDFSPSEVESALLAGFAPVSLGESRLRTETAGLVACQWIHTLQACYRIG 247
                                    12        22        32        42        52        62        72        82       |92|      102       112       122       132       142       152       162        |-    |  182       192       202       212       222       232       242     
                                                       31-MSE                                                     90-MSE                                  131-MSE                                 171   177                                                                      
                                                                                                                     93-MSE                                                                                                                                                      


Chain B from PDB  Type:PROTEIN  Length:238
 aligned with B2RH75_PORG3 | B2RH75 from UniProtKB/TrEMBL  Length:248

    Alignment length:243
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242   
         B2RH75_PORG3     3 LPLFYAPDIEQSDRLPDDEAGHILRVLRMQAGDRLRLTDGRGSFFDAVIETADRKSCYVSVCGQESWQKPWRDRITIAIAPTKQSERMEWMLEKLVEIGVDEVVFIESEHSERRRIKAERLERIAISAMKQSLKASFPVIRVNIPIQTVIADTPKAAVRLIAYVDEAVRAEITQGRGYPSDFYHVGQDVLILIGPEGDFSPSEVESALLAGFAPVSLGESRLRTETAGLVACQWIHTLQACYR 245
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -------------Methyltrans_RNA-3kw2B01 B:16-239                                                                                                                                                                                                ------ Pfam domains (1)
           Pfam domains (2) -------------Methyltrans_RNA-3kw2B02 B:16-239                                                                                                                                                                                                ------ Pfam domains (2)
         Sec.struct. author ..eee..........hhhhhhhhhh........eeeee....eeeeeeeeee....eeeeeeeeee........eeeee....hhhhhhhhhhhhhhhh..eeeeee.........hhhhhhhhhhhhhhhh......eeeeeeehhhhhhhh....eeeee.......-----...hhhhh......eeeee......hhhhhhhhhhhh.eee.......hhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3kw2 B   3 LPLFYAPDIEQSDRLPDDEAGHILRVLRmQAGDRLRLTDGRGSFFDAVIETADRKSCYVSVCGQESWQKPWRDRITIAIAPTKQSERmEWmLEKLVEIGVDEVVFIESEHSERRRIKAERLERIAISAmKQSLKASFPVIRVNIPIQTVIADTPKAAVRLIAYVDEAVR-----GRGYPSDFYHVGQDVLILIGPEGDFSPSEVESALLAGFAPVSLGESRLRTETAGLVACQWIHTLQACYR 245
                                    12        22        32        42        52        62        72        82       |92|      102       112       122       132       142       152       162        |-    |  182       192       202       212       222       232       242   
                                                       31-MSE                                                     90-MSE                                  131-MSE                                 171   177                                                                    
                                                                                                                     93-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 3KW2)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3KW2)

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Clan: SPOUT (28)

(-) Gene Ontology  (5, 5)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (B2RH75_PORG3 | B2RH75)
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.
    GO:0006364    rRNA processing    Any process involved in the conversion of a primary ribosomal RNA (rRNA) transcript into one or more mature rRNA molecules.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

 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
    ADN  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MSE  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 3kw2)
 

(-) 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
  3kw2
    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
  B2RH75_PORG3 | B2RH75
    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
  B2RH75_PORG3 | B2RH75
    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 3KW2)

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 3KW2)