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 :  CRYSTAL STRUCTURE OF AN UNCHARACTERIZED CONSERVED PROTEIN FROM MYCOBACTERIUM TUBERCULOSIS
 
Authors :  J. B. Bonanno, M. Rutter, K. T. Bain, S. Chang, S. Ozyurt, S. Wasserman, J. M. Sauder, S. K. Burley, S. C. Almo, New York Sgx Research Center For Structural Genomics (Nysgxrc)
Date :  13 Mar 09  (Deposition) - 24 Mar 09  (Release) - 24 Mar 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.50
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Structural Genomics, Unknown Function, Cell Membrane, Membrane, Transmembrane, Psi-2, Protein Structure Initiative, New York Sgx Research Center For Structural Genomics, Nysgxrc (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. B. Bonanno, M. Rutter, K. T. Bain, S. Chang, S. Ozyurt, S. Wasserman, J. M. Sauder, S. K. Burley, S. C. Almo
Crystal Structure Of An Uncharacterized Conserved Protein From Mycobacterium Tuberculosis
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - UNCHARACTERIZED PROTEIN RV1825/MT1873
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: MODIFIED PET26
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 562
    Expression System Vector: PET
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 134-292
    Gene: RV1825, MT1873, MTCY1A11.18C
    Organism Scientific: MYCOBACTERIUM TUBERCULOSIS
    Organism Taxid: 1773

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 3GMG)

(-) Sites  (0, 0)

(no "Site" information available for 3GMG)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Gly A:176 -Pro A:177
2Pro A:232 -Pro A:233
3Gly B:176 -Pro B:177
4Pro B:232 -Pro B:233

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3GMG)

(-) 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:143
 aligned with Y1825_MYCTO | P9WFG2 from UniProtKB/Swiss-Prot  Length:292

    Alignment length:143
                                   158       168       178       188       198       208       218       228       238       248       258       268       278       288   
          Y1825_MYCTO   149 ARLAALSILVGAVGATGPGVMITIDDPGPGVAPEVMIDVINELRAAGAEAIQINDAHRSVRVGVDTWVVGVPGSLTVDTKVLSPPYSILAIGDPPTLAAAMNIPGGAQDGVKRVGGRMVVQQADRVDVTALRQPKQHQYAQPV 291
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhh....eeeeeeeeeee......hhhhhhhhhhhhhhh...eeeee....eee......eeee..eeee..eee...eeeeee.hhhhhhhhhh...hhhhhhhhh..eeeeeeeeeeee............ee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3gmg A 149 ARLAALSILVGAVGATGPGVMITIDDPGPGVAPEVMIDVINELRAAGAEAIQINDAHRSVRVGVDTWVVGVPGSLTVDTKVLSPPYSILAIGDPPTLAAAMNIPGGAQDGVKRVGGRMVVQQADRVDVTALRQPKQHQYAQPV 291
                                   158       168       178       188       198       208       218       228       238       248       258       268       278       288   


Chain A from PDB  Type:PROTEIN  Length:143
 aligned with Y1825_MYCTU | P9WFG3 from UniProtKB/Swiss-Prot  Length:292

    Alignment length:143
                                   158       168       178       188       198       208       218       228       238       248       258       268       278       288   
          Y1825_MYCTU   149 ARLAALSILVGAVGATGPGVMITIDDPGPGVAPEVMIDVINELRAAGAEAIQINDAHRSVRVGVDTWVVGVPGSLTVDTKVLSPPYSILAIGDPPTLAAAMNIPGGAQDGVKRVGGRMVVQQADRVDVTALRQPKQHQYAQPV 291
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhh....eeeeeeeeeee......hhhhhhhhhhhhhhh...eeeee....eee......eeee..eeee..eee...eeeeee.hhhhhhhhhh...hhhhhhhhh..eeeeeeeeeeee............ee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3gmg A 149 ARLAALSILVGAVGATGPGVMITIDDPGPGVAPEVMIDVINELRAAGAEAIQINDAHRSVRVGVDTWVVGVPGSLTVDTKVLSPPYSILAIGDPPTLAAAMNIPGGAQDGVKRVGGRMVVQQADRVDVTALRQPKQHQYAQPV 291
                                   158       168       178       188       198       208       218       228       238       248       258       268       278       288   


Chain B from PDB  Type:PROTEIN  Length:143
 aligned with Y1825_MYCTO | P9WFG2 from UniProtKB/Swiss-Prot  Length:292

    Alignment length:143
                                   158       168       178       188       198       208       218       228       238       248       258       268       278       288   
          Y1825_MYCTO   149 ARLAALSILVGAVGATGPGVMITIDDPGPGVAPEVMIDVINELRAAGAEAIQINDAHRSVRVGVDTWVVGVPGSLTVDTKVLSPPYSILAIGDPPTLAAAMNIPGGAQDGVKRVGGRMVVQQADRVDVTALRQPKQHQYAQPV 291
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhh....eeeeeeeeeee......hhhhhhhhhhhhhhh...eeeee....eee......eeee..eeee..eee...eeeeee.hhhhhhhhhh....hhhhhhh...eeeeeeeeeeee............ee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3gmg B 149 ARLAALSILVGAVGATGPGVMITIDDPGPGVAPEVMIDVINELRAAGAEAIQINDAHRSVRVGVDTWVVGVPGSLTVDTKVLSPPYSILAIGDPPTLAAAMNIPGGAQDGVKRVGGRMVVQQADRVDVTALRQPKQHQYAQPV 291
                                   158       168       178       188       198       208       218       228       238       248       258       268       278       288   


Chain B from PDB  Type:PROTEIN  Length:143
 aligned with Y1825_MYCTU | P9WFG3 from UniProtKB/Swiss-Prot  Length:292

    Alignment length:143
                                   158       168       178       188       198       208       218       228       238       248       258       268       278       288   
          Y1825_MYCTU   149 ARLAALSILVGAVGATGPGVMITIDDPGPGVAPEVMIDVINELRAAGAEAIQINDAHRSVRVGVDTWVVGVPGSLTVDTKVLSPPYSILAIGDPPTLAAAMNIPGGAQDGVKRVGGRMVVQQADRVDVTALRQPKQHQYAQPV 291
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhh....eeeeeeeeeee......hhhhhhhhhhhhhhh...eeeee....eee......eeee..eeee..eee...eeeeee.hhhhhhhhhh....hhhhhhh...eeeeeeeeeeee............ee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3gmg B 149 ARLAALSILVGAVGATGPGVMITIDDPGPGVAPEVMIDVINELRAAGAEAIQINDAHRSVRVGVDTWVVGVPGSLTVDTKVLSPPYSILAIGDPPTLAAAMNIPGGAQDGVKRVGGRMVVQQADRVDVTALRQPKQHQYAQPV 291
                                   158       168       178       188       198       208       218       228       238       248       258       268       278       288
   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 3GMG)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3GMG)

(-) Gene Ontology  (5, 8)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (Y1825_MYCTU | P9WFG3)
cellular component
    GO:0005576    extracellular region    The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.
    GO:0016021    integral component of membrane    The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    GO:0005887    integral component of plasma membrane    The component of the plasma membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0005886    plasma membrane    The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

Chain A,B   (Y1825_MYCTO | P9WFG2)
cellular component
    GO:0016021    integral component of membrane    The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0005886    plasma membrane    The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

 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
(no "Ligands, Modified Residues, Ions" information available for 3gmg)
 
  Sites
(no "Sites" information available for 3gmg)
 
  Cis Peptide Bonds
    Gly A:176 - Pro A:177   [ RasMol ]  
    Gly B:176 - Pro B:177   [ RasMol ]  
    Pro A:232 - Pro A:233   [ RasMol ]  
    Pro B:232 - Pro B:233   [ 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 ](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
  3gmg
    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
  Y1825_MYCTO | P9WFG2
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
  Y1825_MYCTU | P9WFG3
    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
  Y1825_MYCTO | P9WFG2
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)
  Y1825_MYCTU | P9WFG3
    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 3GMG)

(-) Related Entries Specified in the PDB File

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