Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asymmetric Unit
(-)Biological Unit 1
collapse expand < >
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)

(-) Description

Title :  STRUCTURE OF B. SUBTILIS PURS C2 CRYSTAL FORM
 
Authors :  R. Anand, A. A. Hoskins, E. M. Bennett, M. D. Sintchak, J. Stubbe, S. E. Ea
Date :  28 Apr 04  (Deposition) - 14 Sep 04  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (2x)
Keywords :  Purs, Tetramer, Complex Formyl Glycinamide Synthetase, Fgar, Fgam, Structural Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. Anand, A. A. Hoskins, E. M. Bennett, M. D. Sintchak, J. Stubbe, S. E. Ealick
A Model For The Bacillus Subtilis Formylglycinamide Ribonucleotide Amidotransferase Multiprotein Complex.
Biochemistry V. 43 10343 2004
PubMed-ID: 15301532  |  Reference-DOI: 10.1021/BI0491292

(-) Compounds

Molecule 1 - PURS
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET 11A
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: YEXA, BSU06460
    Organism Scientific: BACILLUS SUBTILIS
    Organism Taxid: 1423

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 8)

Asymmetric Unit (1, 8)
No.NameCountTypeFull Name
1MSE8Mod. Amino AcidSELENOMETHIONINE
Biological Unit 1 (1, 16)
No.NameCountTypeFull Name
1MSE16Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (0, 0)

(no "Site" information available for 1T4A)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1T4A)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1T4A)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1T4A)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1T4A)

(-) Exons   (0, 0)

(no "Exon" information available for 1T4A)

(-) 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:80
 aligned with PURS_BACSU | P12049 from UniProtKB/Swiss-Prot  Length:84

    Alignment length:80
                                    10        20        30        40        50        60        70        80
            PURS_BACSU    1 MYKVKVYVSLKESVLDPQGSAVQHALHSMTYNEVQDVRIGKYMELTIEKSDRDLDVLVKEMCEKLLANTVIEDYRYEVEE 80
               SCOP domains d1t4aa_ A: PurS subunit of FGAM synthetase                                       SCOP domains
               CATH domains -1t4aA00 A:2-80  [code=3.30.1280.10, no name defined]                            CATH domains
               Pfam domains -------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeee.....hhhhhhhhhhhhhh....eeeeeeeeeeeeee.....hhhhhhhhhhhhh......eeeeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------- Transcript
                  1t4a A  1 mYKVKVYVSLKESVLDPQGSAVQHALHSmTYNEVQDVRIGKYmELTIEKSDRDLDVLVKEmCEKLLANTVIEDYRYEVEE 80
                            |       10        20        30        40  |     50        60|       70        80
                            |                          29-MSE        43-MSE            61-MSE               
                            1-MSE                                                                           


Chain B from PDB  Type:PROTEIN  Length:80
 aligned with PURS_BACSU | P12049 from UniProtKB/Swiss-Prot  Length:84

    Alignment length:80
                                    10        20        30        40        50        60        70        80
            PURS_BACSU    1 MYKVKVYVSLKESVLDPQGSAVQHALHSMTYNEVQDVRIGKYMELTIEKSDRDLDVLVKEMCEKLLANTVIEDYRYEVEE 80
               SCOP domains d1t4ab_ B: PurS subunit of FGAM synthetase                                       SCOP domains
               CATH domains -1t4aB00 B:2-80  [code=3.30.1280.10, no name defined]                            CATH domains
               Pfam domains -------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeee.....hhhhhhhhhhhhhh....eeeeeeeeeeeeee.....hhhhhhhhhhhhh......eeeeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------- Transcript
                  1t4a B  1 mYKVKVYVSLKESVLDPQGSAVQHALHSmTYNEVQDVRIGKYmELTIEKSDRDLDVLVKEmCEKLLANTVIEDYRYEVEE 80
                            |       10        20        30        40  |     50        60|       70        80
                            1-MSE                      29-MSE        43-MSE            61-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  (1, 2)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1T4A)

(-) Gene Ontology  (7, 7)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (PURS_BACSU | P12049)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0016874    ligase activity    Catalysis of the joining of two substances, or two groups within a single molecule, with the concomitant hydrolysis of the diphosphate bond in ATP or a similar triphosphate.
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
    GO:0004642    phosphoribosylformylglycinamidine synthase activity    Catalysis of the reaction: N(2)-formyl-N(1)-(5-phospho-D-ribosyl)glycinamide + L-glutamine + ATP + H(2)O = 2-(formamido)-N(1)-(5-phospho-D-ribosyl)acetamidine + L-glutamate + ADP + 2 H(+) + phosphate.
biological process
    GO:0006189    'de novo' IMP biosynthetic process    The chemical reactions and pathways resulting in the formation of IMP, inosine monophosphate, by the stepwise assembly of a purine ring on ribose 5-phosphate.
    GO:0006164    purine nucleotide biosynthetic process    The chemical reactions and pathways resulting in the formation of a purine nucleotide, a compound consisting of nucleoside (a purine base linked to a deoxyribose or ribose sugar) esterified with a phosphate group at either the 3' or 5'-hydroxyl group of the sugar.
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 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 1t4a)
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1t4a)
 
Biological Unit
  Complete Structure
    Biological Unit 1  [ 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 ](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
  1t4a
    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
  PURS_BACSU | P12049
    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
  PURS_BACSU | P12049
    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
        PURS_BACSU | P12049: 1twj

(-) Related Entries Specified in the PDB File

1gtd