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(-) Description

Title :  PUTATIVE PREVENT-HOST-DEATH PROTEIN FROM NITROSOMONAS EUROPAEA
 
Authors :  J. Osipiuk, T. Skarina, O. Kagan, A. Savchenko, A. Edwards, A. Joachimi Midwest Center For Structural Genomics (Mcsg)
Date :  22 Dec 06  (Deposition) - 23 Jan 07  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.40
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Biol. Unit 3:  A (2x),B (2x),C (2x),D (2x)
Keywords :  Prevent-Host-Death Protein, Structural Genomics, Apc7367, Psi-2, Protein Structure Initiative, Midwest Center For Structural Genomics, Mcsg, Unknown Function (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Osipiuk, T. Skarina, O. Kagan, A. Savchenko, A. Edwards, A. Joachimiak
Crsytal Structure Of Putative Prevent-Host-Death Protein From Nitrosomonas Europaea.
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - HYPOTHETICAL PROTEIN
    Atcc: 19718
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET15B
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: NE2111
    Organism Scientific: NITROSOMONAS EUROPAEA
    Organism Taxid: 915

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): AB  
Biological Unit 2 (1x):   CD
Biological Unit 3 (2x): A (2x)B (2x)C (2x)D (2x)

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 6)

Asymmetric Unit (3, 6)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
2MSE3Mod. Amino AcidSELENOMETHIONINE
3SO42Ligand/IonSULFATE ION
Biological Unit 1 (2, 2)
No.NameCountTypeFull Name
1GOL-1Ligand/IonGLYCEROL
2MSE1Mod. Amino AcidSELENOMETHIONINE
3SO41Ligand/IonSULFATE ION
Biological Unit 2 (3, 4)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
2MSE2Mod. Amino AcidSELENOMETHIONINE
3SO41Ligand/IonSULFATE ION
Biological Unit 3 (2, 4)
No.NameCountTypeFull Name
1GOL-1Ligand/IonGLYCEROL
2MSE2Mod. Amino AcidSELENOMETHIONINE
3SO42Ligand/IonSULFATE ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:42 , ARG A:46 , PRO C:40 , ILE C:41 , GLY C:42 , GLU C:43 , ARG C:46 , HOH C:404 , HOH C:428 , HOH C:441 , ARG D:31BINDING SITE FOR RESIDUE SO4 C 401
2AC2SOFTWAREPRO B:40 , ILE B:41 , GLY B:42 , GLU B:43 , ARG B:46 , HOH B:420 , HOH B:445 , HOH B:452 , ARG C:31BINDING SITE FOR RESIDUE SO4 B 402
3AC3SOFTWAREARG A:31 , HOH A:100 , ILE D:21 , PRO D:40 , ILE D:41 , GLY D:42 , GLU D:43 , ARG D:46BINDING SITE FOR RESIDUE GOL D 400

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2ODK)

(-) 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:51
 aligned with Q82T22_NITEU | Q82T22 from UniProtKB/TrEMBL  Length:85

    Alignment length:51
                                    10        20        30        40        50 
          Q82T22_NITEU    1 MHVWPVQDAKARFSEFLDACITEGPQIVSRRGAEEAVLVPIGEWRRLQAAA 51
               SCOP domains d2odka1 A:1-51 Hypothetical protein NE2111          SCOP domains
               CATH domains -2odkA00 A:2-51 YefM-like domain                    CATH domains
               Pfam domains --------------------------------------------------- Pfam domains
         Sec.struct. author ..eeehhhhhhhhhhhhhhhhhh..eeeee..eeeeeeeehhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------- Transcript
                  2odk A  1 mHVWPVQDAKARFSEFLDACITEGPQIVSRRGAEEAVLVPIGEWRRLQAAA 51
                            |       10        20        30        40        50 
                            |                                                  
                            1-MSE                                              


Chain B from PDB  Type:PROTEIN  Length:50
 aligned with Q82T22_NITEU | Q82T22 from UniProtKB/TrEMBL  Length:85

    Alignment length:50
                                    11        21        31        41        51
          Q82T22_NITEU    2 HVWPVQDAKARFSEFLDACITEGPQIVSRRGAEEAVLVPIGEWRRLQAAA 51
               SCOP domains d2odkb_ B: Hypothetical protein NE2111             SCOP domains
               CATH domains 2odkB00 B:2-51 YefM-like domain                    CATH domains
               Pfam domains -------------------------------------------------- Pfam domains
         Sec.struct. author .eeehhhhhhhhhhhhhhhhhhh.eeeee..eeeeeeeehhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------- Transcript
                  2odk B  2 HVWPVQDAKARFSEFLDACITEGPQIVSRRGAEEAVLVPIGEWRRLQAAA 51
                                    11        21        31        41        51


Chain C from PDB  Type:PROTEIN  Length:51
 aligned with Q82T22_NITEU | Q82T22 from UniProtKB/TrEMBL  Length:85

    Alignment length:51
                                    10        20        30        40        50 
          Q82T22_NITEU    1 MHVWPVQDAKARFSEFLDACITEGPQIVSRRGAEEAVLVPIGEWRRLQAAA 51
               SCOP domains d2odkc_ C: Hypothetical protein NE2111              SCOP domains
               CATH domains -2odkC00 C:2-51 YefM-like domain                    CATH domains
               Pfam domains --------------------------------------------------- Pfam domains
         Sec.struct. author ..eeehhhhhhhhhhhhhhhhhh..eeeee..eeeeeeeehhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------- Transcript
                  2odk C  1 mHVWPVQDAKARFSEFLDACITEGPQIVSRRGAEEAVLVPIGEWRRLQAAA 51
                            |       10        20        30        40        50 
                            1-MSE                                              


Chain D from PDB  Type:PROTEIN  Length:52
 aligned with Q82T22_NITEU | Q82T22 from UniProtKB/TrEMBL  Length:85

    Alignment length:52
                             1                                                  
                             |       9        19        29        39        49  
          Q82T22_NITEU    - -MHVWPVQDAKARFSEFLDACITEGPQIVSRRGAEEAVLVPIGEWRRLQAAA 51
               SCOP domains d2odkd_ D: Hypothetical protein NE2111               SCOP domains
               CATH domains 2odkD00 D:0-51 YefM-like domain                      CATH domains
           Pfam domains (1) -PhdYeFM_antitox-2odkD01 D:1-51                      Pfam domains (1)
           Pfam domains (2) -PhdYeFM_antitox-2odkD02 D:1-51                      Pfam domains (2)
           Pfam domains (3) -PhdYeFM_antitox-2odkD03 D:1-51                      Pfam domains (3)
           Pfam domains (4) -PhdYeFM_antitox-2odkD04 D:1-51                      Pfam domains (4)
         Sec.struct. author ...eeehhhhhhhhhhhhhhhhhh..eeeee..eeeeeeeehhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------- Transcript
                  2odk D  0 HmHVWPVQDAKARFSEFLDACITEGPQIVSRRGAEEAVLVPIGEWRRLQAAA 51
                             |       9        19        29        39        49  
                             1-MSE
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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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) (23004)

(-) CATH Domains  (1, 4)

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

(-) Pfam Domains  (1, 4)

Asymmetric Unit
(-)
Clan: Plasmid_toxin (9)

(-) Gene Ontology  (0, 0)

Asymmetric Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 2ODK)

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