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(-) Description

Title :  CRYSTAL STRUCTURE OF A NTF-2 LIKE PROTEIN OF UNKNOWN FUNCTION (SPO1084) FROM SILICIBACTER POMEROYI DSS-3 AT 1.69 A RESOLUTION
 
Authors :  Joint Center For Structural Genomics (Jcsg)
Date :  16 Dec 08  (Deposition) - 24 Feb 09  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.69
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Ntf2-Like Protein, Structural Genomics, Joint Center For Structural Genomics, Jcsg, Protein Structure Initiative, Psi-2, Unknown Function (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Joint Center For Structural Genomics (Jcsg)
Crystal Structure Of Ntf-2 Like Protein Of Unknown Function (Yp_166335. 1) From Silicibacter Pomeroyi Dss-3 At 1. 69 A Resolution
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - UNCHARACTERIZED NTF-2 LIKE PROTEIN
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: SPEEDET
    Expression System Strain: HK100
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: SPO1084, YP_166335.1
    Organism Scientific: SILICIBACTER POMEROYI DSS-3
    Organism Taxid: 246200

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 43)

Asymmetric/Biological Unit (4, 43)
No.NameCountTypeFull Name
1ACT3Ligand/IonACETATE ION
2EDO7Ligand/Ion1,2-ETHANEDIOL
3MSE24Mod. Amino AcidSELENOMETHIONINE
4UNL9Ligand/IonUNKNOWN LIGAND

(-) Sites  (19, 19)

Asymmetric Unit (19, 19)
No.NameEvidenceResiduesDescription
01AC1SOFTWARETYR A:17 , MSE A:21 , GLU A:39 , ASN A:89 , PHE A:96 , ASP A:98 , LYS A:114 , UNL A:121BINDING SITE FOR RESIDUE UNL A 120
02AC2SOFTWAREMSE A:21 , GLU A:39 , PHE A:55 , MSE A:58 , CYS A:59 , TYR A:116 , UNL A:120BINDING SITE FOR RESIDUE UNL A 121
03AC3SOFTWAREGLU A:30 , ARG A:110 , HOH A:145 , HOH A:317 , ALA B:54 , ALA B:57 , MSE B:58 , ASP B:61 , HOH B:354BINDING SITE FOR RESIDUE ACT A 122
04AC4SOFTWAREASP A:90 , GLY A:93 , MSE A:94 , ARG A:95 , HOH A:387 , PRO D:27 , HOH D:339BINDING SITE FOR RESIDUE ACT A 123
05AC5SOFTWAREGLY A:35 , LYS A:36 , TRP B:49 , GLU B:60 , ASP B:61 , HOH B:226BINDING SITE FOR RESIDUE EDO A 124
06AC6SOFTWAREGLY A:35 , LYS A:36 , EDO A:126 , HOH A:177 , HOH A:430 , ASP B:61 , ALA B:62 , HOH B:284BINDING SITE FOR RESIDUE EDO A 125
07AC7SOFTWAREGLY A:35 , SER A:51 , ARG A:52 , ASP A:53 , EDO A:125 , HOH A:177 , HOH A:208BINDING SITE FOR RESIDUE EDO A 126
08AC8SOFTWAREARG A:31 , HOH A:158 , HOH A:265 , HOH A:371 , ALA B:57 , HOH B:384BINDING SITE FOR RESIDUE EDO A 127
09AC9SOFTWAREMSE B:21 , GLU B:39 , ASN B:89 , PHE B:96 , ASP B:98 , LYS B:114 , UNL B:122BINDING SITE FOR RESIDUE UNL B 120
10BC1SOFTWAREMSE B:21 , GLU B:39 , MSE B:58 , CYS B:59 , TRP B:91 , LYS B:114 , UNL B:122 , HOH B:491BINDING SITE FOR RESIDUE UNL B 121
11BC2SOFTWAREGLU B:39 , TYR B:43 , LEU B:48 , ASN B:50 , TYR B:116 , UNL B:120 , UNL B:121BINDING SITE FOR RESIDUE UNL B 122
12BC3SOFTWAREARG B:110 , EDO B:124 , HOH B:186 , GLY C:35 , HOH C:349BINDING SITE FOR RESIDUE ACT B 123
13BC4SOFTWAREARG B:31 , SER B:108 , TRP B:109 , ACT B:123 , HOH B:196 , LYS C:36BINDING SITE FOR RESIDUE EDO B 124
14BC5SOFTWARETRP A:49 , GLY B:35 , LYS B:36 , HOH B:303BINDING SITE FOR RESIDUE EDO B 125
15BC6SOFTWARETYR C:17 , MSE C:21 , ASN C:89 , PHE C:96 , ASP C:98 , LYS C:114 , UNL C:121BINDING SITE FOR RESIDUE UNL C 120
16BC7SOFTWAREMSE C:21 , GLU C:39 , TYR C:43 , LEU C:48 , MSE C:58 , TRP C:91 , TYR C:116 , UNL C:120BINDING SITE FOR RESIDUE UNL C 121
17BC8SOFTWAREMSE D:21 , GLU D:39 , TYR D:43 , LEU D:48 , ASN D:50 , MSE D:58 , TRP D:91 , LYS D:114 , TYR D:116 , UNL D:121BINDING SITE FOR RESIDUE UNL D 120
18BC9SOFTWARETYR D:17 , MSE D:21 , ASN D:89 , PHE D:96 , ASP D:98 , LYS D:114 , UNL D:120BINDING SITE FOR RESIDUE UNL D 121
19CC1SOFTWAREGLY B:107 , SER B:108 , HOH B:437 , TRP D:49 , SER D:51 , HOH D:124 , HOH D:239BINDING SITE FOR RESIDUE EDO D 122

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3FKA)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3FKA)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3FKA)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3FKA)

(-) Exons   (0, 0)

(no "Exon" information available for 3FKA)

(-) 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:119
 aligned with Q5LUH0_RUEPO | Q5LUH0 from UniProtKB/TrEMBL  Length:119

    Alignment length:119
                                    10        20        30        40        50        60        70        80        90       100       110         
         Q5LUH0_RUEPO     1 MTTSEHIAALTALVETYVMAMTRGDRPALERIFFGKASEVGHYEGELLWNSRDAFIAMCEDAADAETDPFWAISSVSVQGDIAMLHVENDWAGMRFDDFLTVLLHEGSWRIVSKVYRIR 119
               SCOP domains ----------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhheeeeeeeeeee..eeeeeehhhhhhhhhhhh.......eeeeeeeee..eeeeeeeeee..eeeeeeeeeeee..eeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------- Transcript
                 3fka A   1 mTTSEHIAALTALVETYVmAmTRGDRPALERIFFGKASEVGHYEGELLWNSRDAFIAmCEDAADAETDPFWAISSVSVQGDIAmLHVENDWAGmRFDDFLTVLLHEGSWRIVSKVYRIR 119
                            |       10        20|       30        40        50       |60        70        80   |    90   |   100       110         
                            |                19-MSE                                 58-MSE                    84-MSE    94-MSE                     
                            1-MSE              21-MSE                                                                                              


Chain B from PDB  Type:PROTEIN  Length:120
 aligned with Q5LUH0_RUEPO | Q5LUH0 from UniProtKB/TrEMBL  Length:119

    Alignment length:120
                             1                                                                                                                      
                             |       9        19        29        39        49        59        69        79        89        99       109       119
         Q5LUH0_RUEPO     - -MTTSEHIAALTALVETYVMAMTRGDRPALERIFFGKASEVGHYEGELLWNSRDAFIAMCEDAADAETDPFWAISSVSVQGDIAMLHVENDWAGMRFDDFLTVLLHEGSWRIVSKVYRIR 119
               SCOP domains ------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhheeeeeeeeeee..eeeeeehhhhhhhhhhhh.......eeeeeeeee..eeeeeeeeee..eeeeeeeeeeee..eeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------ Transcript
                 3fka B   0 GmTTSEHIAALTALVETYVmAmTRGDRPALERIFFGKASEVGHYEGELLWNSRDAFIAmCEDAADAETDPFWAISSVSVQGDIAmLHVENDWAGmRFDDFLTVLLHEGSWRIVSKVYRIR 119
                             |       9        19 |      29        39        49        59        69        79    |   89    |   99       109       119
                             1-MSE            19-MSE                                 58-MSE                    84-MSE    94-MSE                     
                                                21-MSE                                                                                              


Chain C from PDB  Type:PROTEIN  Length:119
 aligned with Q5LUH0_RUEPO | Q5LUH0 from UniProtKB/TrEMBL  Length:119

    Alignment length:119
                                    10        20        30        40        50        60        70        80        90       100       110         
         Q5LUH0_RUEPO     1 MTTSEHIAALTALVETYVMAMTRGDRPALERIFFGKASEVGHYEGELLWNSRDAFIAMCEDAADAETDPFWAISSVSVQGDIAMLHVENDWAGMRFDDFLTVLLHEGSWRIVSKVYRIR 119
               SCOP domains ----------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhheeeeeeeeeee..eeeeeehhhhhhhhhhhh.......eeeeeeeee..eeeeeeeeee..eeeeeeeeeeee..eeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------- Transcript
                 3fka C   1 mTTSEHIAALTALVETYVmAmTRGDRPALERIFFGKASEVGHYEGELLWNSRDAFIAmCEDAADAETDPFWAISSVSVQGDIAmLHVENDWAGmRFDDFLTVLLHEGSWRIVSKVYRIR 119
                            |       10        20|       30        40        50       |60        70        80   |    90   |   100       110         
                            1-MSE            19-MSE                                 58-MSE                    84-MSE    94-MSE                     
                                               21-MSE                                                                                              


Chain D from PDB  Type:PROTEIN  Length:119
 aligned with Q5LUH0_RUEPO | Q5LUH0 from UniProtKB/TrEMBL  Length:119

    Alignment length:119
                                    10        20        30        40        50        60        70        80        90       100       110         
         Q5LUH0_RUEPO     1 MTTSEHIAALTALVETYVMAMTRGDRPALERIFFGKASEVGHYEGELLWNSRDAFIAMCEDAADAETDPFWAISSVSVQGDIAMLHVENDWAGMRFDDFLTVLLHEGSWRIVSKVYRIR 119
               SCOP domains ----------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhheeeeeeeeeee..eeeeeehhhhhhhhhhh........eeeeeeeee..eeeeeeeeee..eeeeeeeeeeee..eeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------- Transcript
                 3fka D   1 mTTSEHIAALTALVETYVmAmTRGDRPALERIFFGKASEVGHYEGELLWNSRDAFIAmCEDAADAETDPFWAISSVSVQGDIAmLHVENDWAGmRFDDFLTVLLHEGSWRIVSKVYRIR 119
                            |       10        20|       30        40        50       |60        70        80   |    90   |   100       110         
                            1-MSE            19-MSE                                 58-MSE                    84-MSE    94-MSE                     
                                               21-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  (0, 0)

(no "SCOP Domain" information available for 3FKA)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3FKA)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3FKA)

(-) Gene Ontology  (3, 3)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C,D   (Q5LUH0_RUEPO | Q5LUH0)
molecular function
    GO:0003674    molecular_function    Elemental activities, such as catalysis or binding, describing the actions of a gene product at the molecular level. A given gene product may exhibit one or more molecular functions.
biological process
    GO:0008150    biological_process    Any process specifically pertinent to the functioning of integrated living units: cells, tissues, organs, and organisms. A process is a collection of molecular events with a defined beginning and end.
cellular component
    GO:0005575    cellular_component    The part of a cell, extracellular environment or virus in which a gene product is located. A gene product may be located in one or more parts of a cell and its location may be as specific as a particular macromolecular complex, that is, a stable, persistent association of macromolecules that function together.

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