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(-) Description

Title :  CRYSTAL STRUCTURE OF YERB PROTEIN FROM BACILLUS SUBTILIS. NORTHEAST STRUCTURAL GENOMICS TARGET SR586
 
Authors :  J. Seetharaman, Y. Chen, F. Forouhar, D. Wang, Y. Fang, K. Cunningham, L-C. Ma, R. Xia, J. Liu, M. C. Baran, T. B. Acton, B. Rost, G. T. Montelione, J. F. Hunt, L. Tong, Northeast Structural Genomics Consortium (Nesg)
Date :  04 May 07  (Deposition) - 15 May 07  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym./Biol. Unit :  A
Keywords :  Yerb Protein, Structural Genomics, Psi-2, Protein Structure Initiative, Northeast Structural Genomics Consortium, Nesg, Unknown Function (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Seetharaman, Y. Chen, F. Forouhar, D. Wang, Y. Fang, K. Cunningham, L-C. Ma, R. Xia, J. Liu, M. C. Baran, T. B. Acton, B. Rost, G. T. Montelione, J. F. Hunt, L. Tong
Crystal Structure Of Yerb Protein From Bacillus Subtilis.
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - YERB PROTEIN
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET21
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: YERB, BSU06570
    Organism Scientific: BACILLUS SUBTILIS
    Organism Taxid: 1423
    Strain: 168

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 3)

Asymmetric/Biological Unit (1, 3)
No.NameCountTypeFull Name
1MSE3Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (0, 0)

(no "Site" information available for 2PSB)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2PSB)

(-) Cis Peptide Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1Arg A:44 -Pro A:45
2Gly A:80 -Pro A:81
3Pro A:139 -Pro A:140

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2PSB)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2PSB)

(-) Exons   (0, 0)

(no "Exon" information available for 2PSB)

(-) 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:290
 aligned with YERB_BACSU | O34968 from UniProtKB/Swiss-Prot  Length:331

    Alignment length:296
                                    41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321      
           YERB_BACSU    32 KLKAPLTGLKTEQKVTERRPVAVVVNNHPKARPQSGLSKADIVIEALAEGQITRFLAIFQSQMPETVGPVRSAREYFVTLSNGFDSIFVHHGWSPGAKKQLESGAADYMNGLDFDGSLFWRADFSKPPHNSYTSYDYIKKAAEQKGYKLKQETNPLLFQTSDAKPANESYNVRVDYGTNNVTNLVEYNYDKKAEFYTRSSDGVITTDRETGKPVAMQNIFIVEASHHIIDQDGRRDIDLESGGKGLLFQHGNVIETDWKQVNGRIVPVKDGKWLPFVPGKTWINIVPDLDAASISK 327
               SCOP domains d2psba1 A:13-308 Uncharacterized protein YerB                                                                                                                                                                                                                                                            SCOP domains
               CATH domains 2psbA00 A:13-308 YerB-like domain                                                                                                                                                                                                                                                                        CATH domains
               Pfam domains ----DUF3048-2psbA01 A:17-295                                                                                                                                                                                                                                                               ------------- Pfam domains
         Sec.struct. author ...........hhhhhhh..eeeee..hhhhh.........eeeeee.....eeeeeee......ee......hhhhhhhhhh...eeee...hhhhhhhhhh....eeehhhhh....ee.........eeeehhhhhhhhhhhh..............------....eeeee........eeeeeee....eeeeee..ee.............eeeeee.eeee......eeee....eeeeeee..eeeeeeeeee..eeeeee..ee.......eeeeee.hhh.eeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2psb A  13 KLKAPLTGLKTEQKVTERRPVAVVVNNHPKARPQSGLSKADIVIEALAEGQITRFLAIFQSQmPETVGPVRSAREYFVTLSNGFDSIFVHHGWSPGAKKQLESGAADYmNGLDFDGSLFWRADFSKPPHNSYTSYDYIKKAAEQKGYKLKQETNPLLFQT------NESYNVRVDYGTNNVTNLVEYNYDKKAEFYTRSSDGVITTDRETGKPVAmQNIFIVEASHHIIDQDGRRDIDLESGGKGLLFQHGNVIETDWKQVNGRIVPVKDGKWLPFVPGKTWINIVPDLDAASISK 308
                                    22        32        42        52        62        72  |     82        92       102       112       122       132       142       152       162       172      |182       192       202       212       222     | 232       242       252       262       272       282       292       302      
                                                                                         75-MSE                                       121-MSE                                            172    179                                              228-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, 1)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (1, 1)

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

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Clan: no clan defined [family: DUF3048] (1)

(-) Gene Ontology  (2, 2)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (YERB_BACSU | O34968)
cellular component
    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.

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