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(-) Description

Title :  CRYSTAL STRUCTURE OF HYPOTHETICAL PROTEIN, PH0823
 
Authors :  T. Hosaka, S. Kishishita, K. Murayama, M. Shirouzu, Riken Structural Genomics/Proteomics Initiative (Rsgi)
Date :  24 Jul 06  (Deposition) - 24 Jan 07  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.75
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,D  (1x)
Biol. Unit 2:  B,C  (1x)
Keywords :  Conserved Hypothetical Protein, Putative Universal Protein A, Structural Genomics, Nppsfa, National Project On Protein Structural And Functional Analyses, Riken Structural Genomics/Proteomics Initiative, Rsgi, Unknown Function (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. Hosaka, S. Kishishita, K. Murayama, M. Shirouzu, S. Yokoyama
Crystal Structure Of Hypothetical Protein, Ph0823
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - HYPOTHETICAL PROTEIN PH0823
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET11A
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Organism Scientific: PYROCOCCUS HORIKOSHII
    Organism Taxid: 70601
    Strain: OT3

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): A  D
Biological Unit 2 (1x):  BC 

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 2DUM)

(-) Sites  (0, 0)

(no "Site" information available for 2DUM)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2DUM)

(-) 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:143
 aligned with O58553_PYRHO | O58553 from UniProtKB/TrEMBL  Length:170

    Alignment length:157
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       
         O58553_PYRHO     4 MFRKVLFPTDFSEGAYRAVEVFEKRNKMEVGEVILLHVIDEGTLEELMDGYSFFYDNAEIELKDIKEKLKEEASRKLQEKAEEVKRAFRAKNVRTIIRFGIPWDEIVKVAEEENVSLIILPSRGKLSLSHEFLGSTVMRVLRKTKKPVLIIKEVDEN 160
               SCOP domains d2duma_ A: automated matches                                                                                                                                  SCOP domains
               CATH domains 2dumA00 A:4-160 Tyrosyl-Transfer RNA Synthetase             , subunit E, domain 1                                                                             CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee...hhhhhhhhhhhhhhh.....eeeeeeeee.hhhhh..------------....hhhhhhhhhhhhhhhhhhhhhhhh...eeeeeeeeehhhhhhhhhhhhh...eeeee....--......hhhhhhhhhhh...eeee...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2dum A   4 MFRKVLFPTDFSEGAYRAVEVFEKRNKMEVGEVILLHVIDEGTLEELM------------ELKDIKEKLKEEASRKLQEKAEEVKRAFRAKNVRTIIRFGIPWDEIVKVAEEENVSLIILPSRGK--LSHEFLGSTVMRVLRKTKKPVLIIKEVDEN 160
                                    13        23        33        43       | -         -|       73        83        93       103       113       123    |  133       143       153       
                                                                          51           64                                                             128  |                             
                                                                                                                                                         131                             


Chain B from PDB  Type:PROTEIN  Length:139
 aligned with O58553_PYRHO | O58553 from UniProtKB/TrEMBL  Length:170

    Alignment length:156
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153      
         O58553_PYRHO     4 MFRKVLFPTDFSEGAYRAVEVFEKRNKMEVGEVILLHVIDEGTLEELMDGYSFFYDNAEIELKDIKEKLKEEASRKLQEKAEEVKRAFRAKNVRTIIRFGIPWDEIVKVAEEENVSLIILPSRGKLSLSHEFLGSTVMRVLRKTKKPVLIIKEVDE 159
               SCOP domains d2dumb_ B: automated matches                                                                                                                                 SCOP domains
               CATH domains 2dumB00 B:4-159 Tyrosyl-Transfer RNA Synthetase , s           ubunit E, domain 1                                                                             CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....eeee...hhhhhhhhhhhhhhh...eeeeeeeeeee.hhhhhhhhh.-----------.hhhhhhhhhhhhhhhhhhhhhhhhh.eeeeeeeeeeehhhhhhhhhhhhh...eeeee..------....hhhhhhhhhhh...eeee..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2dum B   4 MFRKVLFPTDFSEGAYRAVEVFEKRNKMEVGEVILLHVIDEGTLEELMDGY-----------KDIKEKLKEEASRKLQEKAEEVKRAFRAKNVRTIIRFGIPWDEIVKVAEEENVSLIILPSR------HEFLGSTVMRVLRKTKKPVLIIKEVDE 159
                                    13        23        33        43        53|        -  |     73        83        93       103       113       123  |    133       143       153      
                                                                             54          66                                                         126    133                          


Chain C from PDB  Type:PROTEIN  Length:146
 aligned with O58553_PYRHO | O58553 from UniProtKB/TrEMBL  Length:170

    Alignment length:158
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153        
         O58553_PYRHO     4 MFRKVLFPTDFSEGAYRAVEVFEKRNKMEVGEVILLHVIDEGTLEELMDGYSFFYDNAEIELKDIKEKLKEEASRKLQEKAEEVKRAFRAKNVRTIIRFGIPWDEIVKVAEEENVSLIILPSRGKLSLSHEFLGSTVMRVLRKTKKPVLIIKEVDENE 161
               SCOP domains d2dumc_ C: automated matches                                                                                                                                   SCOP domains
               CATH domains 2dumC00 C:4-161 Tyrosyl-Transfer RNA Synthetase ,             subunit E, domain 1                                                                              CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee...hhhhhhhhhhhhhhh.....eeeeeeeee.hhh.....------------.hhhhhhhhhhhhhhhhhhhhhhhhhh...eeeeeeeeehhhhhhhhhhhhhh..eeeee............hhhhhhhhhhh...eeee....... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2dum C   4 MFRKVLFPTDFSEGAYRAVEVFEKRNKMEVGEVILLHVIDEGTLEELMD------------LKDIKEKLKEEASRKLQEKAEEVKRAFRAKNVRTIIRFGIPWDEIVKVAEEENVSLIILPSRGKLSLSHEFLGSTVMRVLRKTKKPVLIIKEVDENE 161
                                    13        23        33        43        |-         - |      73        83        93       103       113       123       133       143       153        
                                                                           52           65                                                                                                


Chain D from PDB  Type:PROTEIN  Length:141
 aligned with O58553_PYRHO | O58553 from UniProtKB/TrEMBL  Length:170

    Alignment length:156
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153      
         O58553_PYRHO     4 MFRKVLFPTDFSEGAYRAVEVFEKRNKMEVGEVILLHVIDEGTLEELMDGYSFFYDNAEIELKDIKEKLKEEASRKLQEKAEEVKRAFRAKNVRTIIRFGIPWDEIVKVAEEENVSLIILPSRGKLSLSHEFLGSTVMRVLRKTKKPVLIIKEVDE 159
               SCOP domains d2dumd_ D: automated matches                                                                                                                                 SCOP domains
               CATH domains 2dumD00 D:4-159 Tyrosyl-Transfer RNA Synthetase ,            subunit E, domain 1                                                                             CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeeee...hhhhhhhhhhhhhhh...eeeeeeeeeeehhhhhhhh..-----------...hhhhhhhhhhhhhhhhhhhhhhhh.eeeeeeeeeeehhhhhhhhhhhhh...eeeee....----....hhhhhhhhhhh...eeee..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2dum D   4 MFRKVLFPTDFSEGAYRAVEVFEKRNKMEVGEVILLHVIDEGTLEELMDG-----------LKDIKEKLKEEASRKLQEKAEEVKRAFRAKNVRTIIRFGIPWDEIVKVAEEENVSLIILPSRGK----HEFLGSTVMRVLRKTKKPVLIIKEVDE 159
                                    13        23        33        43        53         - |      73        83        93       103       113       123    |  133       143       153      
                                                                            53          65                                                            128  133
   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  (1, 4)

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

(-) CATH Domains  (1, 4)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (1, 1)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (O58553_PYRHO | O58553)
biological process
    GO:0006950    response to stress    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a disturbance in organismal or cellular homeostasis, usually, but not necessarily, exogenous (e.g. temperature, humidity, ionizing radiation).

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