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(-) Description

Title :  CRYSTAL STRUCTURE OF A PREDICTED CODING REGION AF_0060 FROM ARCHAEOGLOBUS FULGIDUS DSM 4304
 
Authors :  B. Nocek, X. Xu, Y. Koniyenko, A. Yakounine, A. Savchenko, A. Edwards, A. Joachimiak, Midwest Center For Structural Genomics (Mcsg)
Date :  28 Feb 07  (Deposition) - 27 Mar 07  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (2x)
Keywords :  Mcsg, Psi2, Mad, Structural Genomics, Singleton, Predicted Coding Region Af_0060, Protein Structure Initiative, Midwest Center For Structural Genomics, Unknown Function (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  B. Nocek, X. Xu, A. Savchenko, A. Edwards, A. Joachimiak
Crystal Structure Of A Predicted Coding Region Af_0060 From Archaeoglobus Fulgidus Dsm 4304
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - HYPOTHETICAL PROTEIN AF_0060
    Atcc: 49558
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET15B
    Expression System Strain: BL21-GOLD(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: AF_0060
    Organism Scientific: ARCHAEOGLOBUS FULGIDUS DSM 4304
    Organism Taxid: 224325
    Strain: DSM 4304, VC-16, JCM 9628, NBRC 100126

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (2x): AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 13)

Asymmetric Unit (3, 13)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
2MG2Ligand/IonMAGNESIUM ION
3MSE10Mod. Amino AcidSELENOMETHIONINE
Biological Unit 1 (2, 22)
No.NameCountTypeFull Name
1GOL2Ligand/IonGLYCEROL
2MG-1Ligand/IonMAGNESIUM ION
3MSE20Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:47 , GLU A:50 , GLU A:66 , ASP A:69 , HOH A:154BINDING SITE FOR RESIDUE MG A 101
2AC2SOFTWAREGLU B:47 , GLU B:50 , GLU B:66 , ASP B:69 , HOH B:121 , HOH B:160BINDING SITE FOR RESIDUE MG B 101
3AC3SOFTWAREARG A:30 , HOH A:143 , ARG B:5BINDING SITE FOR RESIDUE GOL A 102

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2P06)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2P06)

 Sequence-Structure Mapping

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(-) PROSITE Motifs  (0, 0)

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(-) Exons   (0, 0)

(no "Exon" information available for 2P06)

(-) 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:84
 aligned with Y060_ARCFU | O30176 from UniProtKB/Swiss-Prot  Length:93

    Alignment length:84
                                    10        20        30        40        50        60        70        80    
            Y060_ARCFU    1 MDYFRLAEKFLREMHAKYMKRVSRPGNTPRPWFDFSEERLLSRLFEEMDELREAVEKEDWENLRDELLDVANFCMYLWGKLSVK 84
               SCOP domains d2p06a1 A:1-84 Hypothetical protein AF0060                                           SCOP domains
               CATH domains -2p06A00 A:2-84 all-alpha NTP pyrophosphatases                                       CATH domains
               Pfam domains ------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------ Transcript
                  2p06 A  1 mDYFRLAEKFLREmHAKYmKRVSRPGNTPRPWFDFSEERLLSRLFEEmDELREAVEKEDWENLRDELLDVANFCmYLWGKLSVK 84
                            |       10   |    20        30        40       |50        60        70    |   80    
                            |           14-MSE|                           48-MSE                     75-MSE     
                            1-MSE            19-MSE                                                             


Chain B from PDB  Type:PROTEIN  Length:88
 aligned with Y060_ARCFU | O30176 from UniProtKB/Swiss-Prot  Length:93

    Alignment length:88
                                 1                                                                                  
                                 |   5        15        25        35        45        55        65        75        
            Y060_ARCFU    - -----MDYFRLAEKFLREMHAKYMKRVSRPGNTPRPWFDFSEERLLSRLFEEMDELREAVEKEDWENLRDELLDVANFCMYLWGKLSV 83
               SCOP domains -----d2p06b1 B:1-83 Hypothetical protein AF0060                                          SCOP domains
               CATH domains 2p06B00 B:-4-83 all-alpha NTP pyrophosphatases                                           CATH domains
           Pfam domains (1) ---------------------------------------MazG-2p06B01 B:35-83                              Pfam domains (1)
           Pfam domains (2) ---------------------------------------MazG-2p06B02 B:35-83                              Pfam domains (2)
         Sec.struct. author ....hhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------- Transcript
                  2p06 B -4 LYFQGmDYFRLAEKFLREmHAKYmKRVSRPGNTPRPWFDFSEERLLSRLFEEmDELREAVEKEDWENLRDELLDVANFCmYLWGKLSV 83
                                 |   5        15   |    25        35        45  |     55        65        75        
                                 1-MSE       14-MSE|                           48-MSE                     75-MSE    
                                                  19-MSE
   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, 2)

Asymmetric Unit
(-)
Class: All alpha proteins (14657)

(-) CATH Domains  (1, 2)

Asymmetric Unit
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Clan: MazG (25)

(-) Gene Ontology  (0, 0)

Asymmetric Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 2P06)

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