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(-) Description

Title :  STRUCTURE OF AN EXPANSIN LIKE PROTEIN FROM BACILLUS SUBTILIS AT 1.9A RESOLUTION
 
Authors :  F. Kerff, S. Petrella, R. Herman, E. Sauvage, B. Joris, P. Charlier
Date :  09 May 08  (Deposition) - 14 Oct 08  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym./Biol. Unit :  A
Keywords :  Bacillus Subtilis, Expansin, Peptidoglycan Associated Protein, Unknown Function, Mlta, Bacteria Autolysis, Peptidoglycan-Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  F. Kerff, A. Amoroso, R. Herman, E. Sauvage, S. Petrella, P. Filee, P. Charlier, B. Joris, A. Tabuchi, N. Nikolaidis, D. J. Cosgrove
Crystal Structure And Activity Of Bacillus Subtilis Yoaj (Exlx1), A Bacterial Expansin That Promotes Root Colonization.
Proc. Natl. Acad. Sci. Usa V. 105 16876 2008
PubMed-ID: 18971341  |  Reference-DOI: 10.1073/PNAS.0809382105

(-) Compounds

Molecule 1 - EXPANSIN LIKE PROTEIN
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET22B
    Expression System Strain: BL21 (DE3-PLYS)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: YOAJ, BSU18630
    Organism Scientific: BACILLUS SUBTILIS
    Organism Taxid: 1423
    Strain: 168
    Synonym: YOAJ

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

Asymmetric/Biological Unit (2, 4)
No.NameCountTypeFull Name
1FMT3Ligand/IonFORMIC ACID
2GOL1Ligand/IonGLYCEROL

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:60 , PRO A:61 , ASN A:100 , LYS A:102BINDING SITE FOR RESIDUE GOL A 209
2AC2SOFTWARELYS A:95 , SER A:192 , GLY A:193 , HOH A:290 , HOH A:382BINDING SITE FOR RESIDUE FMT A 210
3AC3SOFTWARELYS A:48 , MET A:155 , ASP A:156 , HOH A:428BINDING SITE FOR RESIDUE FMT A 211
4AC4SOFTWAREARG A:117 , THR A:199 , HOH A:236BINDING SITE FOR RESIDUE FMT A 212

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3D30)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Asp A:26 -Pro A:27

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3D30)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3D30)

(-) Exons   (0, 0)

(no "Exon" information available for 3D30)

(-) 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:208
 aligned with YOAJ_BACSU | O34918 from UniProtKB/Swiss-Prot  Length:232

    Alignment length:208
                                    34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224        
           YOAJ_BACSU    25 AAYDDLHEGYATYTGSGYSGGAFLLDPIPSDMEITAINPADLNYGGVKAALAGSYLEVEGPKGKTTVYVTDLYPEGARGALDLSPNAFRKIGNMKDGKINIKWRVVKAPITGNFTYRIKEGSSRWWAAIQVRNHKYPVMKMEYEKDGKWINMEKMDYNHFVSTNLGTGSLKVRMTDIRGKVVKDTIPKLPESGTSKAYTVPGHVQFPE 232
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeeeee....................eeeehhhhhhhhhh.......eeeeee..eeeeeeeeee........eeehhhhhhhhhhhhhh.eeeeeeee........eeee.......eeeeeee.....eeeeeeee..eeeeeee.....eeee......eeeeeee....eeeeee...........eeee....... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3d30 A   1 MAYDDLHEGYATYTGSGYSGGAFLLDPIPSDMEITAINPADLNYGGVKAALAGSYLEVEGPKGKTTVYVTDLYPEGARGALDLSPNAFRKIGNMKDGKINIKWRVVKAPITGNFTYRIKEGSSRWWAAIQVRNHKYPVMKMEYEKDGKWINMEKMDYNHFVSTNLGTGSLKVRMTDIRGKVVKDTIPKLPESGTSKAYTVPGHVQFPE 208
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200
   Legend:   → Mismatch (orange background)
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  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 3D30)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3D30)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3D30)

(-) Gene Ontology  (2, 2)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (YOAJ_BACSU | O34918)
cellular component
    GO:0005618    cell wall    The rigid or semi-rigid envelope lying outside the cell membrane of plant, fungal, most prokaryotic cells and some protozoan parasites, maintaining their shape and protecting them from osmotic lysis. In plants it is made of cellulose and, often, lignin; in fungi it is composed largely of polysaccharides; in bacteria it is composed of peptidoglycan; in protozoan parasites such as Giardia species, it's made of carbohydrates and proteins.
    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.

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 Related Entries

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

UniProtKB/Swiss-Prot
        YOAJ_BACSU | O34918: 2bh0 4fer 4fft 4fg2 4fg4

(-) Related Entries Specified in the PDB File

2bh0 CRYSTAL STRUCTURE OF A SEMET DERIVATIVE OF EXPA FROM BACILLUS SUBTILIS