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(-) Description

Title :  X-RAY CRYSTAL STRUCTURE OF PROTEIN YOPX FROM BACILLUS SUBTILIS. NORTHEAST STRUCTURAL GENOMICS CONSORTIUM TARGET SR411.
 
Authors :  S. M. Vorobiev, W. Zhou, J. Seetharaman, F. Forouhar, A. A. Kuzin, C. K. Ho, H. Janjua, K. Cunningham, L. C. Ma, R. Xiao, J. Liu, T. Acton, G. T. Montelione, J. F. Hunt, L. Tong, Northeast Structural Genomics Consortium (Nesg)
Date :  16 Aug 06  (Deposition) - 29 Aug 06  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.80
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C  (2x)
Keywords :  Nesg, Sr411, Yopx, O34401, Structural Genomics, Psi-2, Protein Structure Initiative, Northeast Structural Genomics Consortium, Unknown Function (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. M. Vorobiev, W. Zhou, J. Seetharaman, F. Forouhar, A. A. Kuzin, C. K. Ho, K. Cunningham, L. C. Ma, R. Xiao, J. Liu, T. Acton, G. T. Montelione, J. F. Hunt, L. Tong
Crystal Structure Of The Hypothetical Protein Yopx From Bacillus Subtilis
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - YOPX PROTEIN
    Chains: A, B, C
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET21
    Expression System Strain: BL21(DE3)+MAGIC
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: YOPX
    Organism Scientific: BACILLUS SUBTILIS
    Organism Taxid: 1423
    Strain: 168

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit : ABC
Biological Unit 1 (1x): AB 
Biological Unit 2 (2x):   C

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 9)

Asymmetric Unit (1, 9)
No.NameCountTypeFull Name
1MSE9Mod. Amino AcidSELENOMETHIONINE
Biological Unit 1 (1, 6)
No.NameCountTypeFull Name
1MSE6Mod. Amino AcidSELENOMETHIONINE
Biological Unit 2 (1, 6)
No.NameCountTypeFull Name
1MSE6Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (0, 0)

(no "Site" information available for 2I2L)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2I2L)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2I2L)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2I2L)

(-) PROSITE Motifs  (0, 0)

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(-) Exons   (0, 0)

(no "Exon" information available for 2I2L)

(-) 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:130
 aligned with YOPX_BACSU | O34401 from UniProtKB/Swiss-Prot  Length:134

    Alignment length:134
                                    10        20        30        40        50        60        70        80        90       100       110       120       130    
           YOPX_BACSU     1 MNTAYRVWDGEQMHYWDDEGLSLIIKSNGDWTLKRLYTDVLVPVVDSTNRNAALMWGAKVRGKFIYDRSIVKITSDDKESSDVCEVKFSDGVFQVDVSKISADYDVTAVGWVEYATIEVIGDVYQNPELLEGVK 134
               SCOP domains d2i2la1 A:1-134 Hypothetical protein YopX                                                                                              SCOP domains
               CATH domains -----------------------------------------------------2i2lA02 A:54-124  [code=2.30.30.100, no name d    efined]              ---------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeee....eee......eeee.....eeeeee....eeeeee......eeee.eee..eee..eeeeeee........eee.eee..eeeee...----..eee.hhh..eeeeeeee............ Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2i2l A   1 mNTAYRVWDGEQmHYWDDEGLSLIIKSNGDWTLKRLYTDVLVPVVDSTNRNAALmWGAKVRGKFIYDRSIVKITSDDKESSDVCEVKFSDGVFQVDVSK----YDVTAVGWVEYATIEVIGDVYQNPELLEGVK 134
                            |       10  |     20        30        40        50    |   60        70        80        90        |-   |   110       120       130    
                            |          13-MSE                                    55-MSE                                      99  104                              
                            1-MSE                                                                                                                                 


Chain B from PDB  Type:PROTEIN  Length:133
 aligned with YOPX_BACSU | O34401 from UniProtKB/Swiss-Prot  Length:134

    Alignment length:136
                                                                                                                                                               134  
                                    10        20        30        40        50        60        70        80        90       100       110       120       130   |  
           YOPX_BACSU     1 MNTAYRVWDGEQMHYWDDEGLSLIIKSNGDWTLKRLYTDVLVPVVDSTNRNAALMWGAKVRGKFIYDRSIVKITSDDKESSDVCEVKFSDGVFQVDVSKISADYDVTAVGWVEYATIEVIGDVYQNPELLEGVK--   -
               SCOP domains d2i2lb_ B: Hypothetical protein YopX                                                                                                     SCOP domains
               CATH domains -----------------------------------------------------2i2lB02 B:54-124  [code=2.30.30.100, no name d   efined]               ------------ CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeee....eee.....eeeee.....eeeeee....eeeeee......eeee.eee..eee..eeeeeee......eeeee.eee..eeeee...---...eee.hhh..ee..eeee.............. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2i2l B   1 mNTAYRVWDGEQmHYWDDEGLSLIIKSNGDWTLKRLYTDVLVPVVDSTNRNAALmWGAKVRGKFIYDRSIVKITSDDKESSDVCEVKFSDGVFQVDVSK---DYDVTAVGWVEYATIEVIGDVYQNPELLEGVKLE 136
                            |       10  |     20        30        40        50    |   60        70        80        90        |-  |    110       120       130      
                            1-MSE      13-MSE                                    55-MSE                                      99 103                                 


Chain C from PDB  Type:PROTEIN  Length:128
 aligned with YOPX_BACSU | O34401 from UniProtKB/Swiss-Prot  Length:134

    Alignment length:131
                                    10        20        30        40        50        60        70        80        90       100       110       120       130 
           YOPX_BACSU     1 MNTAYRVWDGEQMHYWDDEGLSLIIKSNGDWTLKRLYTDVLVPVVDSTNRNAALMWGAKVRGKFIYDRSIVKITSDDKESSDVCEVKFSDGVFQVDVSKISADYDVTAVGWVEYATIEVIGDVYQNPELLE 131
               SCOP domains d2i2lc_ C: Hypothetical protein YopX                                                                                                SCOP domains
               CATH domains -----------------------------------------------------2i2lC02 C:54-124  [code=2.30.30.100, no name d   efined]               ------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeee....eee.....eeeee.....eeeeee....eeeeee......eeeeeeee..eeee..eeeeeee.....eeeeeeeee..eeeee...---...eee......eeeeeeee......... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2i2l C   1 mNTAYRVWDGEQmHYWDDEGLSLIIKSNGDWTLKRLYTDVLVPVVDSTNRNAALmWGAKVRGKFIYDRSIVKITSDDKESSDVCEVKFSDGVFQVDVSK---DYDVTAVGWVEYATIEVIGDVYQNPELLE 131
                            |       10  |     20        30        40        50    |   60        70        80        90        |-  |    110       120       130 
                            1-MSE      13-MSE                                    55-MSE                                      99 103
   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, 3)

Asymmetric Unit
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (1, 3)

Asymmetric Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2I2L)

(-) Gene Ontology  (0, 0)

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